Ammonia oxidization is a critical process in nitrogen cycling that involves ammonia oxidizing archaea (AOA) and bacteria (AOB). However, the effects of different manure amounts on ammonia-oxidizing microorganisms (AOMs) over the course of organic vegetables production remains unclear. We used theamoAgene to evaluated AOMs abundance and community structure in organic vegetable fields. Quantitative PCR revealed that AOB were more abundant than AOA. Among them, theamoAcopy number of AOB treated with 900 kgN ha−1was 21.3 times that of AOA. The potential nitrification rate was significantly correlated with AOB abundance (P< 0.0001) but not with AOA, suggesting that AOB might contribute more to nitrification than AOA. AOB sequences were classified intoNitrosomonasandNitrosospira,and AOA intoNitrosopumilusandNitrososphaera.NitrosomonasandNitrosopumiluswere predominant in treatments that received manure nitrogen at ≥ 900 kg ha−1(52.7–56.5%) and when manure was added (72.7–99.8%), respectively, whereasNitrosospiraandNitrososphaeraoccupied more than a half percentage in those that received ≤ 600 kg ha−1(58.4–84.9%) and no manure (59.6%). A similar manure rate resulted in more identical AOMs’ community structures than greater difference manure rate. The bacterialamoAgene abundances and ratios of AOB and AOA showed significantly positive correlations with soil electrical conductivity, total carbon and nitrogen, nitrate, phosphorus, potassium, and organic carbon, indicating that these were potential key factors influencing AOMs. This study explored the AOMs’ variation in organic vegetable fields in Northwest China and provided a theoretical basis and reference for the subsequent formulation of proper manure management.