Although many studies have explored patterns of fungal community diversity and composition along various environmental gradients, the trends of co-occurrence networks across similar gradients remain elusive. Here, we constructed co-occurrence networks for fungal community along a 2300 m elevation gradient on Mt Norikura, Japan, hypothesizing a progressive decline in network connectivity with elevation due to reduced niche differentiation caused by declining temperature and ecosystem productivity. Results agreed broadly with predictions, with an overall decline in network connectivity with elevation for all fungi and the high abundance phyla. However, trends were not uniform with elevation, most decline in connectivity occurred between 700 m and 1500 m elevation, remaining relatively stable above this. Temperature and precipitation dominated variation in network properties, with lower mean annual temperature (MAT) and higher mean annual precipitation (MAP) at higher elevations giving less network connectivity, largely through indirect effects on soil properties. Among keystone taxa that played crucial roles in network structure, the variation in abundance along the elevation gradient was also controlled by climate and also pH. Our findings point to a major role of climate gradients in mid-latitude mountain areas in controlling network connectivity. Given the importance of the orographic precipitation effect, microbial community trends seen along elevation gradients might not be mirrored by those seen along latitudinal temperature gradients.ImportanceAlthough many studies have explored patterns of fungal community diversity and composition along various environmental gradients, it is unclear how the topological structure of co-occurrence networks shifts across environmental gradients. In this study, we found that the connectivity of the fungal community decreased with increasing elevation, and that climate was the dominant factor regulating co-occurrence patterns, apparently acting indirectly through soil characteristics. Assemblages of keystone taxa playing crucial roles in network structure varied along the elevation gradient and were also largely controlled by climate. Our results provide insight into the shift of soil fungal community co-occurrence structure along elevational gradients, and possible driving mechanisms behind this.Graphic abstract