Fungal communities related to invasive plants may change with an elevational gradient, which may affect the performance and invasiveness of invasive plants. Our recent study revealed that root arbuscular mycorrhizal fungi colonization rate of invasive plant Galinsoga quadriradiata decreased with elevation. However, it is unclear whether it is caused by the changes in the fungal community along elevation. To address this issue, we used high-throughput sequencing techniques, functional groupings and linear statistics to examine how fungal communities in the rhizosphere and roots of G. quadriradiata are changed across the elevation in Qinling and Bashan Mountains, China. Our results revealed that species diversity and composition of the rhizosphere and root fungal communities changed along the elevation. The Shannon–Wiener diversity index in the rhizosphere and roots increased and decreased with elevation, respectively. In contrast, the relative abundance of pathotroph in the rhizosphere decreased while it increased in the roots with elevation. These suggest that, when the invasive plant colonizes into high altitudes, it may not suffer from limited rhizosphere fungal symbionts, but rather the ability of the plant to create and maintain these associations decreases. The invader tends to accumulate more pathogenic fungi in the roots, while the dependence on symbiotic fungi is reduced during expansion into higher elevations. These results highlight that the interactions between invasive plants and fungal community substantially change along elevation, and that belowground interactions may be key in our understanding of how invasive plants derive success in stressful, high-elevation environments.