As a special type of ecological system, the wetlands are very sensitive to global climate change and response to it through special energy and water exchange system and carbon cycles. The microbial community structure in the soils in the marshes at 4 heights above sea level in Nyaiqentanglha Mountains was analyzed by phospholipid fatty acid method and activities of 6 kinds of enzymes (phenol oxidase, urease, peroxidase, protease, L-asparaginase and alkaline phosphatase) was tested in this study. The results showed that the key factor which affected the soil microbial community structure and enzyme activities was mean annual temperature. The indexes of soil physical and chemical properties, soil enzyme activities and soil microbial biomass all significantly decreased with the height above sea level increasing.