Abstract: Field experiments were conducted to determine the change of nutrients and enzyme activities of soil and functional diversity of microbial communities after application of microbial agents. The results showed that microbial agents application treatments increased the content of soil organic carbon, phosphorus and potassium, and among the microbial agents application treatments, the extent of increasing was the largest in the indigenous bacteria propagation agent application treatment with 7.82%, 39.19% and 48.95% increase compared to the control respectively. The content of alkali hydrolysable nitrogen of soil was decreased slightly. The content of soil urease activity was the highest under the mixed application of indigenous bacteria propagation agent, which was 1.03 mg/(g·24 h), and the content of soil invertase activity was the highest under the mixed application of bio-organic fertilizer, which was 70.96 mg/(g·24 h). In addition, microbial agent application treatments with green manure showed increased microbial diversity index and soil respiration rate in different degrees. Therefore, the addition of microbial agents with green manure not only increased the content of soil organic carbon and available nutrients, but also increased functional diversity of microbial communities and enzyme activities of soil, which could be helpful to improve soil fertility. The indigenous bacteria propagation agent application treatments had the optimal effects among microbial agents application treatments.