Nitrogen (N) deposition and precipitation change are important phenomena in global climate change and can greatly influence grassland ecosystems. Soil fungal communities are a functionally diverse group and they mediate many ecological processes as well as influence plant growth and soil health. There have been many studies on the responses of plant and soil bacterial communities to N addition. However, the interactive effects of N and water addition on soil fungal communities remain largely unknown, with these interacting effects having great significance for predicting the future effects of multiple climate factor changes on grassland ecosystems. In the present study, we simulated N deposition and precipitation change by N addition (0, 15, 30, 50, 100, 150, 200, and 300 kg N hm^-2 a^-1) and irrigation (no irrigation and irrigation equivalent to 100 mm extra summer rainfall). Utilizing split-plot design and high-throughput sequencing technology, we evaluated the interactive effects of N and water addition on soil fungal community structure. Statistical analyses showed that N and water addition significantly shifted the composition and relative abundance of soil fungal communities. The dominant fungal phyla were Zygomycota (22.0%-48.9%), Basidiomycota (7.8%-18.5%), Ascomycota (9.4%-20.1%), Glomeromycota (0.7%-3.1%), and Chytridiomycota (0.1%-1.3%). Under normal precipitation, the relative abundance of Zygomycota increased in N1-N50 treatments and decreased in N100-N300 treatments. The relative abundance of Ascomycota increased in the N100-N300 treatments. When water was added, the relative abundance of Zygomycota decreased; however, the relative abundance of Ascomycota showed no significant change. At identical N levels, water addition increased the relative abundance of Zygomycota; however, the relative abundance of Basidiomycota, Ascomycota, Glomeromycota, and Chytridiomycota decreased. The relative abundance of all 5 fungal phyla and 11 fungal Classes shifted significantly under different N and water addition rates. The changes in soil fungal community structure are mainly related to the changes in relative abundance of genus Mortierella, family Entolomataceae, and genus Geastrum. Hence, genus Mortierella, family Entolomataceae and genus Geastrum could be utilized as indicator species to signify changes in soil fungal community structure. The results of Principal Coordinate Analysis (PCoA) also revealed that N and water addition significantly modified the structure of the soil fungal community. Structural equation modeling of the integrated response of the plant-soil-microbe system to N and water addition demonstrated that plant community composition and plant species richness were the main factors causing shifts in the soil fungal community. Soil inorganic N and pH indirectly affected the structure of soil fungal community via the plant community. Overall, N and water addition changed the structure of the soil fungal community by interactively affecting the relative abundance of different soil fungal phyla. Therefore, water addition modified the effects of N addition on the soil fungal community.