Agricultural productivity is significantly impeded by salinization, which also adversely affects the environment. The use of compost as a soil conditioner has been shown to effectively ameliorate saline-alkali soils. Nonetheless, there is a paucity of research investigating the effects of compost on microbial populations within these soils. This study utilized high-throughput sequencing technology to specifically investigate the impact of compost addition on fungal diversity and the composting process in saline-alkali soils. The aim was to elucidate the effects of compost incorporation on the composition, structure, and functional group characteristics of fungal communities in such soils. The findings indicate that fungal diversity varied across different fermentation stages, with the predominant functional microbiota differing at each stage. Ascomycota, Mortierellomycota, and Basidiomycota were identified as the dominant fungal taxa in the soil. FUNGuild analysis predicted that the functional capacity of the rhizosphere soil fungal community was significantly enhanced by saprotrophic fungi in saline-alkali soil, resulting in improved soil quality. The Redundancy Analysis indicated that the main environmental factors affecting the fungal community were soil pH, organic matter, and soil enzymes. The findings from this research could offer a theoretical foundation for enhancing saline-alkali soils with microbial biofertilizers and boosting agricultural productivity.