Recent increases in atmospheric carbon dioxide (CO₂) and temperature relieve their limitations on terrestrial ecosystem productivity, while nutrient availability constrains the increasing plant photosynthesis more intensively. Nitrogen (N) and phosphorus (P) are critical for plant physiological activities and consequently regulates ecosystem productivity. Here, for the first time, we mapped N and P densities and concentrations of leaves, woody stems, roots, litter and soil in forest, shrubland and grassland ecosystems across China, based on an intensive investigation in 4,868 sites, covering species composition, biomass, and nutrient concentrations of different tissues of living plants, litter and soil. Forest, shrubland and grassland ecosystems in China stored 6,803.6 Tg N, with 6,635.2 Tg N (97.5%) fixed in soil (to a depth of one metre), and 27.7 Tg N (0.4%), 57.8 Tg N (0.8%), 71.2 Tg N (1%) and 11.7 Tg N (0.2%) in leaves, stems, roots and litter, respectively. The forest, shrubland and grassland ecosystems in China stored 2,806.0 Tg P, with 2,786.1 Tg P (99.3%) fixed in soil (to a depth of one metre), and 2.7 Tg P (0.1%), 9.4 Tg P (0.3%), 6.7 Tg P (0.2%) and 1.0 Tg P (< 0.1%) in leaves, stems, roots and litter, respectively. Our estimation showed that N pools were low in northern China except Changbai Mountains, Mount Tianshan and Mount Alta, while relatively higher values existed in eastern Qinghai-Tibetan Plateau and Yunnan. P densities in vegetation were higher towards the south and northeast part of China, while soil P density was higher towards the north and west part of China. These patterns of N and P densities could potentially improve existing earth system models and large-scale researches on ecosystem nutrients.