Soil microbes are indispensable in agricultural production, and they respond differently to different fertilization regimes. However, there is limited understating of microbial composition and function responses to an organic fertilizer tea seed meal (TSM) and conventional fertilizer. Here we first reported the change rules and functions of soil microbial community in peach orchard soil after application of compound fertilizer plus urea (CFU) and different amounts (1.25, 2.50, 3.75 and 5.00 kg) of TSM. Compared to CFU, the application of 1.25, 2.50 and 3.75 kg TSM significantly decreased the Chao1 index of bacterial community in peach orchard soil. The Shannon index of bacterial and fungal communities in 2.50 kg TSM treatment was significantly higher than that in CFU. Beta diversity analysis of bacteria and fungi (based on Bray-Curtis matrix and OTUs level) revealed significant structural differences among all five experimental groups (ANOSIM, bacteria: R= 0.665, p = 0.001; fungi: R= 0.996, p = 0.001). The TSM treatments significantly decreased the relative abundances of potentially unfriendly bacteria (Acidothermus, Acidicaldus, Sphingomonas, Candidatus Koribacter and Candidatus Solibacter) and fungi (Fusarium), and significantly increased the relative abundances of potentially beneficial fungi (Trechispora, Sagenomella, Penicillium, Acaulium caviariforme, Leucoagaricus and Chlorophyllum) compared with CFU. These changes were more obvious when the application amount of TSM was 2.50 kg. This study provides insights into the potential of application of TSM as an organic fertilizer in agricultural production.