Wetland vegetation is the material basis for the formation and development of alpine peatlands. Investigating the relationship between species diversity of plant communities and soil organic carbon (SOC) helps understanding carbon pool source-sink dynamics in alpine peatlands. This study conducted in Zoige Plateau alpine peatlands employed the community survey method to explore changes in species diversity of plant communities and SOC across different habitats and their relationship. Results indicated that from the peatland center to the edge, alpine peatland community types underwent succession as follows: Carex atrofusca community, Carex muliensis + Equisetum fluviatile community, Blysmus sinocompressus + Carex muliensis community, Kobresia kansuensis + Blysmus sinocompressus community, and Kobresia tibetica + Deschampsia cespitosa community. The SOC, water level, soil water content, and biomass of Cyperaceae plants decreased, while community coverage, density, and soil available nitrogen increased. The Shannon–Wiener index and Pielou index increased, while Simpson index decreased. The water level, soil water content, and soil available nitrogen were the main factors influencing the spatial distribution patterns of plant communities. The community density, coverage, biomass of Cyperaceae plants, and water level were the main factors influencing species diversity of plant communities. SOC was highly significantly positively correlated with Simpson index, and negatively correlated with Shannon–Wiener index and Pielou index (p ≤ 0.01). As water level dropped and waterlogged extent diminished, grass hummock microtopography transitioned from spotted to ridged and then to massed. Habitat filtering and environmental stress caused dominant species succession and species diversity of plant communities to change, resulting in SOC content and the quality of carbon pool to decrease in alpine peatlands.