Stellera chamaejasme is one of the most serious weeds in Qinhai-Tibetan Plateau, the rapid expansion of which exerts an increasing effect on the alpine meadow ecosystem. With high-throughput sequencing technology, geostatistics and GIS method, the spatial heterogeneity of soil fungal diversity in Stellera occurrence area and the spatial correlation between Stellera coverage and soil fungal diversity were investigated in a typical degraded alpine meadow of the Qilian Mountain. Compared to no-Stellera area, the fungi richness in Stellera area decreased, the dominance increased, and the α-diversity reduced. The difference of fungal species composition enhanced and β-diversity significantly increased. The spatial pattern of soil fungal diversity was affected by the invasion of Stellera, resulting in higher fragmentation in occurrence area. Spatial heterogeneity of species composition increased remarkably, and spatial stability of α-diversity and β-diversity decreased. The portion of positive correlation and negative correlation interlaced, indicating no clear spatial correlation between Stellera coverage and soil fungal diversity. Our results indicate that the spatial pattern of soil fungal diversity was affected by the interaction of soil and vegetation in Stellera invaded meadows.