Abstract: In order to understand the changes and influencing factors of the functional gene abundance of nitrification and denitrification microorganisms during the natural recovery process of secondary forests, by using the method of space instead of time, 5, 8, 21, 27, 40 years of natural recovering secondary forest and more than 100 years of primeval forest ( the control group CK) were selected as the research objects, and then the abundance changes of the functional genes such as AOA, AOB and the denitrification functional genes such as NarG, NirK, NirS and NosZ genes which were involved in the nitrification process in the surface soil (0-10 cm) and their relationships with the soil physical and chemical properties were studied. The results showed that AOA gene dominated the nitrification process in the soil at the recovery stage, and the pH and ammonium nitrogen content were the factors affecting the abundance change of AOA gene, which further supported the view that AOA was suitable for low pH and low concentration of NH₄⁺. The abundance of the denitrification functional genes was mainly affected by AOB gene and the soil C/N, and the abundance ratio of (NirK+NirS)/NosZ was less than 1, indicating that the natural recovering secondary forest could better maintain the nitrogen in the soil and reduce the emission of N₂O in the soil. With the natural recovering time of secondary forest, the gradual accumulation of nitrogen and carbon nutrients provided abundant substrates and energy sources for the microbial activities, and the microbial activities were also gradually recovered. The above results showed that the natural recovering secondary forest could better maintain the soil fertility and had higher ecosystem functions.