Alpine wetlands are sensitive and alert to climate change and human activity. Exploring the relationships between the plant diversity and environmental factors are important to understand the biodiversity maintenance mechanism, and for the protection and management of alpine wetlands. In this study, the methods of line transect survey and plot survey were combined to study the influence of water level and hommock microtopography on species diversity of plant communities in Bayanbulak alpine marshes. A total of 39 plant species belonging to 19 families and 22 genera were identified in Bayanbulak alpine marshes. Species composition and richness were significantly affected by the surface water level. Species richness decreased significantly as the surface water level increased (n=11, R~2=0.77, p<0.001). The plant species richness in seasonal water- logged zone was higher than that in perennial water-logged zone, but lower than that in no water-logged zone. The hummock coverage was negatively related to the surface water level (n=11, R~2=0.63, p<0.001), and positively related with species richness (n=11, R~2=0.79, p<0.001). The species richness of the hummock was significantly higher than that of the hollow, and the hummock increased the species richness by 45%. The results indicated that the hommock microtopography could foster high diversity by increasing surface area and by creating multiple micro-habitats.