Soil organic carbon (SOC) fractions are vital intrinsic indicators of SOC stability, and soil fungi are the key drivers of soil carbon cycling. However, variations in SOC fractions along an elevational gradient in mountain meadows and the role of the fungal community in regulating these variations are largely unknown, especially in subtropical areas. In this study, an elevation gradient experiment (with experimental sites at 1500, 1700, and 1900 m) was set up in a Miscanthus sinensis community in a meadow on Wugong Mountain, Southeast China, to clarify the effects of elevation on soil fungal community composition, microbial residue carbon, and SOC fractions. The results showed that the contribution of soil microbial residue carbon to SOC was only 16.1%, and the contribution of soil fungal residue carbon to SOC (15.3%) was far greater than that of bacterial residue carbon (0.3%). An increase in elevation changed the fungal community structure and diversity, especially in the topsoil (0–20 cm depth) compared with that in the subsoil (20–40 cm depth), but did not affect fungal residue carbon in the two soil layers. When separating SOC into the fractions mineral-associated organic carbon (MAOC) and particulate organic carbon (POC), we found that the contribution of MAOC (66.6%) to SOC was significantly higher than that of POC (20.6%). Although an increased elevation did not affect the SOC concentration, it significantly changed the SOC fractions in the topsoil and subsoil. The soil POC concentration and its contribution to SOC increased with an increasing elevation, whereas soil MAOC showed the opposite response. The elevational variations in SOC fractions and the POC/MAOC ratio were co-regulated by the fungal community structure and total nitrogen. Our results suggested that SOC stabilization in mountain meadows decreases with an increasing elevation and is driven by the fungal community structure, providing scientific guidance for SOC sequestration and stability in mountain meadows in subtropical areas.