Water and nitrogen measures affect nitrogen conversion and nitrifying microbial activity in greenhouse soil，but the difference between autotrophic and heterotrophic nitrification under the interactive effects of water and nitrogen remains unclear. From an eight-year long term field experiment of irrigation and nitrogen in greenhouse，the greenhouse soils were used as the experimental soil，and an indoor microcosm experiment was conducted to control soil water holding capacity(WHC)(40% WHC，60% WHC and 80% WHC)and add acetylene inhibits heterotrophic nitrification..The interactive effects of water and nitrogen on soil autotrophic and heterotrophic nitrification rates and ammonia oxidizing microorganisms were explored，and the contribution of ammonia oxidizing microorganisms ammonia-oxidizing archaea(AOA) and ammonia-oxidizing bacteria(AOB) to nitrification was also investigated. The results showed that NH4+-N and NO^3--N contents，copy number of AOA amoA and AOB amoA genes had significant difference in different nitrification pathways under the interactive effects of water and nitrogen...After 7 days incubation without acetylene，NO^3--N content was increased significantly，while NH4+-N content was decreased significantly. The gene abundance of AOA amoA and AOB amoA were increased significantly. After adding acetylene，NO^3--N and NH4+-N content remained constant，the gene abundance of AOA amoA and AOB amoA decreased significantly..The interactive effects of water and nitrogen had a significant effect on the autotrophic and heterotrophic nitrification rates. Redundancy analysis indicated that NH4+-N content，AOB amoA，NO^3--N-C2H2，and AOA amoA could explain 68.9%，34.9%，32.8% and 24.4% of the variation in autotrophic and heterotrophic nitrification rate，respectively. There are two nitrification pathways of autotrophic and heterotrophic nitrification in the greenhouse soils. All nitrogen treatments were dominated by autotrophic nitrification under 60%-80% WHC，accounting for 65%-86% of total nitrification rate..Heterotrophic nitrification was the main nitrification pathway only under 300 and 525 kg·hm-2 treatments of 40%WHC，accounting for 61%-77% of total nitrification rate. Both AOA amoA and AOB amoA can drive the autotrophic nitrification，and AOB amoA has more contribution.