Abstract: The response of soil microbial community is regarded as a sensitive indicator of soil quality changes. A 5-year located experiment was conducted to study the effects of different fertilization regimes on the soil microbial community structure and functional diversity, by using the MicroResp^TM method. The results show that the application of organic fertilizer and biogas slurry at a reasonable rate could significantly promote the metabolic activity of soil microbial community and significantly affect the soil microbial community structure. Long-term application of organic fertilizer and biogas slurry at a high amount such as biogas slurry (HBS) treatment and organic fertilizer (HOM) treatment exhibited negative effects on the soil microbial community structure and functional diversity. Correlation analysis results further indicate that the metabolic activity of soil microbial community was highly correlated with the soil pH, the total phosphorus content and the Cu content, while the Cu content was the main influencing factor. Overall, organic fertilizer application could significantly improve soil nutrient content and lead to an accumulation of heavy metals in soil, thus contributing to the obvious changes in metabolic function of soil microbial community.