1. The intercropping approach of Eucalyptus and native trees has been widely recommended, as an ideal replacement for monoculture Eucalyptus plantations (EUs), to ameliorate global biodiversity loss and mitigate environmental change. However, both suitable native tree species and the best intercropping ratio between Eucalyptus and native trees have not been determined.

2. To fill this gap, a four-level intercropping gradient of Eucalyptus urophylla planted with eight native tree species was set up (i.e., 20%NS, 30%NS, 40%NS, 50%NS), monitored and compared to a monoculture E. urophylla plantation (EU) and a randomly mixed plantation of nine native tree species (NS) in southern China.

3. The results showed that the intercropping ratio of Eucalyptus and native trees had a long-term effect on tree layer structure and health status and a cascading effect on the thermodynamic health state of soil microbes. Shade-tolerant woody species are more suitable for intercropping with Eucalyptus. Intercropping plantations with not less than 30% native trees were more favorable for long-term survival and growth of both planted Eucalyptus and native trees and provided much more favorable conditions for the natural immigration of other native trees, which leads to a healthy plant community with significantly higher eco-exergy compared to EU. The initial mixing ratio between Eucalyptus and high diversity native trees affected soil fertility through its long-term effects on the biodiversity and bio-thermodynamic state of trees and soil microbes.

4. Synthesis and applications. Our results highlight the long-term positive effect of the intercropping ratio of Eucalyptus and high diversity native trees on multi-trophic biodiversity conservation, bio-thermodynamic health development, and soil fertility conservation. In the conversion of monoculture Eucalyptus plantations (EU) to multi-species plantations, it is recommended to mix more than 30% native tree species that have different ecological niches with Eucalyptus.

1. Change of species abundance: Species abundance (Ind/ha) of each tree species in the six types of forest plantations from 2006 (1a) to 2018 (13 a) were given in this file, based on field investigation. Detailed field investigation method is available in our paper which will be published on Journal of Applied Ecology. The average species abundance of each tree was calculated based on three replicated plots for each of the six types of forest plantations. The six forest plantations are monoculture Eucalyptus urophylla plantation (EU); four types of mixed forest plantations of E. urophylla and native tree species (20%NS, 30%NS, 40%NS, 50%NS), and randomly mixed plantation of nine native tree species (NS).

2. Tree layer: Plant biomass density (t/ha), diameter at breast height (DBH, cm), height (m), crown (cm) and mortality (%) for E. urophylla and native trees in the six types of mixed forest plantations were given in this file. Three repetitive plots were investigated for each type of forest plantation. The biomass density of E. urophylla and native trees was calculated by Eqn 1 and 2, respectively. Details can be checked out in the method section of our paper which will be published on Journal of Applied Ecology. The six forest plantations are monoculture Eucalyptus urophylla plantation (EU); four types of mixed forest plantations of E. urophylla and native tree species (20%NS, 30%NS, 40%NS, 50%NS), and randomly mixed plantation of nine native tree species (NS).

3. Plant community: Eco-exergy (KJ/m2), specific eco-exergy (KJ/g), biomass (t/ha), species richness, Shannon-Wiener index, evenness of three plant layers (trees, shrubs and herbs) and the plant community as a whole for the six types of forest plantations, were given in this file based on field investigation done in 2018, 13 years after planting. Three repetitive plots for each type of forest plantation, were investigated. Detailed investigation and calculation methods can be checked out in the method section of our paper which will be published in the Journal of Applied Ecology. The six forest plantations are monoculture Eucalyptus urophylla plantation (EU); four types of mixed forest plantations of E. urophylla and native tree species (20%NS, 30%NS, 40%NS, 50%NS), and randomly mixed plantation of nine native tree species (NS).

4. Soil fauna: Shannon-Wiener, evenness, species richness, abundance (ind/ha), biomass (kg/ha), eco-exergy (KJ/m²), specific eco-exergy(KJ/g) of soil fauna represented here were collected from 0–20 cm soil layer at each plot during the dry and wet seasons, respectively, in 2018, 13 years after planting. Detailed investigation and calculation methods can be checked out in the method section in our paper which will be published in the Journal of Applied Ecology. The six forest plantations are monoculture Eucalyptus urophylla plantation (EU); four types of mixed forest plantations of E. urophylla and native tree species (20%NS, 30%NS, 40%NS, 50%NS), and randomly mixed plantation of nine native tree species (NS).

5. Soil microbial community: Eco-exergy (KJ/m²), specific eco-exergy (KJ/g), and soil microbe phospholipid fatty acids (PLFAs, ng/g) represented here were collected from 0-20 cm soil layer at each plot during the dry and wet seasons, respectively, in 2018, 13 years after planting. The groupings of soil microbe are actinomycetes, arbuscular mycorrhizal fungi (AFM), fungi, general bacteria (GB), gram-negative bacteria (G-), gram-positive bacteria (G+). The sum of the above two specific PLFAs was assumed to represent total fungal abundance. The ratio of fungal to bacterial PLFAs( G-, G+, GB and 15:0, 17:0 ) (F/B) was calculated as an indicator of the microbial community structure. The sum of all PLFAs mentioned above was used to represent the total PLFAs of the soil microbial community. Detailed investigation and calculation methods can be checked out in the method section of our paper which will be published in the Journal of Applied Ecology. The six forest plantations are monoculture Eucalyptus urophylla plantation (EU); four types of mixed forest plantations of E. urophylla and native tree species (20%NS, 30%NS, 40%NS, 50%NS), and randomly mixed plantation of nine native tree species (NS).

6. Soil: SOC (g/kg), NO^-₃-N (mg/kg), NH⁺₄-N (g/kg), AP (mg/kg), AK (mg/kg) were measured for three soil layers (0–20 cm, 20–40 cm, 40–60 cm) at each plot during the dry and wet seasons, respectively, in 2018, 13 years after planting. Detailed investigation and calculation methods can be checked out in the method section in our paper which will be published in the Journal of Applied Ecology. The six forest plantations are monoculture Eucalyptus urophylla plantation (EU); four types of mixed forest plantations of E. urophylla and native tree species (20%NS, 30%NS, 40%NS, 50%NS), and randomly mixed plantation of nine native tree species (NS).

For detailed dataset collection and processing information, please check Wang Y, Lin Y, Zhang L, Liu S, Wang J, Tian Y, Campbell DE, Lin R, Ren H, Lu H. 2023. Long-term effects of intercropping on multi-trophic structure and bio-thermodyanmic health of mixed Eucalyptus-native tree plantations. Journal of Applied Ecology (JAPPL-2023-00679).