Soil fungi play a critical role in the biogeochemical cycles of forest ecosystems. Larix gmelinii is a strong and important timber tree species, which forms close associations with a wide range of soil fungi. However, the temporal-spatial disparity effects on the assembly of soil fungal communities in L. gmelinii forests are poorly understood. To address these questions, a total of 120 samples, including 60 bulk soil and 60 root samples, were collected from Aershan and Genhe in July (summer) and October (autumn)2021. We obtained 7,788 operational taxonomic units (OTUs) after merging, filtering, and rarefying using high-throughput sequencing. The dominant phyla are Basidiomycota, Ascomycota, Mortierellomycota, and Mucoromycota. There were 13 dominant families, among which the families with average relative abundance more than 5% included Thelephoraceae, Mortierellaceae, Archaeorhizomycoaceae, and Inocybaceae. In the functional guilds, symbiotrophic fungi had a relative advantage in the identified functions, and the relative abundances of pathotrophic and saprotrophic fungi varied significantly between sites. There were 12 families differentially expressed across compartments, 10 families differentially expressed between seasons, and 69 families were differentially expressed between sites. The variation in alpha diversity in the bulk soil was greater than that in the rhizosphere soil. Among the three parts (compartment, season, and site), the site had a crucial effect on the beta diversity of the fungal community. Deterministic processes dominated fungal community assembly in Genhe, whereas stochastic processes dominated in Aershan. Soil physicochemical properties and climatic factors significantly affected fungal community structure, among which soil total nitrogen and pH had the greatest effect. This study highlights that spatial variations play a vital role in the structure and assembly of soil fungal communities in L. gmelinii forests, which is of great significance for us in maintaining the health of the forests.