Soil microbial biomass (SMB) C and its seasonal variation have great impact on arid land carbon cycle. Although close correlation of seasonal variation of soil microbial biomass C and carbon cycle were revealed in diverse studies, the relationship in arid land have not been sufficiently studied yet, primarily due to the data poverty of long-term dynamics of soil microbial biomass C. The paper selected four different types of land surfaces, below canopy, litter, lichens, and bare soil, in two typical desert vegetation regions (Haloxylon ammodendron and Tamarix chinensis) in the southern edge of Junggar Basin in western China for revealing seasonal dynamics of soil microbial biomass C in arid lands. Seasonal variations of soil microbial biomass C and surrounding environmental factors under each land surface were monitored from June to October in 2013 for investigating their relationships. The results clearly indicated that the soil microbial biomass C in desert vegetation regions had significant seasonal fluctuations regardless of surface types. Soil microbial biomass C reached the peak point in August in Haloxylon ammodendron plot for all surface types. However, only below canopy in Tamarix chinensis plot peaked at the same time while had the lowest SMB in August for the other three land surface types. Soil microbial biomass C of both typical desert vegetation regions were significantly (P<0.05) related with soil organic matter and total nitrogen through the analysis of soil microbial mass and its impact factors. Furthermore,specific significant impact factors were also identified for different vegetation regions. SMB had a significant positive correlation with soil moisture in the Haloxylon ammodendron plot hut a significant negative correlation with total salt in the Tamarix chinensis plot. Different impact factors resulted in big differences of SMB under the two vegetation cover regions. The results of the study would provide guidance to the research on the responses of SMB to the future climate under different types of vegetation cover regions and different surface types in arid land.