【Objective】This study aimed to investigate the effects of different land use types and soil profiles on ammonia-oxidizing microorganisms and nitrogen (N) cycling processes, with a focus on the community distribution and functional roles of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and complete ammonia oxidizers (Comammox) in agricultural soils under different management regimes.【Method】Soil samples (0-100 cm) were collected from three typical farmland ecosystems in Changshu, Jiangsu Province, including rice-wheat rotation, orchard, and vegetable fields, during both spring and summer. Soil physicochemical properties were determined, and microbial community composition and abundance were analyzed using quantitative PCR and high-throughput sequencing. In addition, microcosm incubation experiments with nitrification inhibitors were conducted to determine nitrification and N2O production rates, enabling clear quantification of microbial contributions to soil nitrogen transformations.【Result】The ammonia oxidation rate and N2O emission rate of the surface soil are the highest, with mean values of 6.1 ± 1.0 mg·kg-1·d-1 (calculated by N, the same as below) and 17.9 ± 6.1 ng·kg-1·d-1, respectively, and both declined significantly with depth. The N2O emission rate in rice–wheat soils (17.5 ± 5.6 ng·kg-1·d-1) was significantly higher than that in vegetable soils (1.5 ± 0.5 ng·kg-1·d-1). Within the rice–wheat system, summer exhibited a significantly higher N2O emission potential than spring. Among ammonia oxidizers, AOB contributed most to nitrification, accounting for 56.6% in surface soils and up to 64.9% in subsurface layers, while the contribution of Comammox increased with depth. Microbial functional gene abundance and diversity showed pronounced vertical heterogeneity and were strongly influenced by land use type. Correlation analysis indicated that microbial gene abundance was significantly positively correlated with nitrification rates, and that ammonium nitrogen and dissolved organic carbon were the key factors regulating both nitrification and N2O emissions. Structural equation modeling further revealed that AOB gene abundance was a major determinant of ammonia oxidation rates and that ammonia oxidation processes were positively linked to N2O emissions.【Conclusion】This study systematically evaluated the effects of land use and soil profile on the functional differentiation of ammonia-oxidizing microorganisms. The findings demonstrated that AOB dominate ammonia oxidation across soil layers, while Comammox play an increasingly important role in deeper soils, and that both groups jointly regulate the potential mechanisms of N2O emissions. These results provide theoretical support for developing microbe-oriented strategies for agricultural nitrogen management.