Although nitrifying and N-fixing functional gene microbes play a crucial role in regulating ecosystem nitrogen (N) cycling, understanding of how N and phosphorus (P) fertilization affect their community structure remains limited. N fertilizer levels were set to simulate N deposition and combined with different P fertilizer levels, to explore the soil-root-shoot physiological indexes, and the response of community structure of N-fixing and nitrifying microorganisms that caused changes in the N cycle of the system to fertilization. The results showed that N and P fertilization significantly decreased soil N pool (NH