To reveal the response of soil microbial community structure to the changes of ground water level, a 200m×300m field experimental site was setup in the beach of Baisha Lake, a typical shallow lake of the Poyang Lake Wetlands. This site included 4 ground water levels:GT-A, GT-B, GT-C, GT-D (moving from shore to center). Phospholipid fatty acids (PLFA) analysis was applied to determine the microbial community structure. Results showed when ground water level raised from GT-A to GT-D, soil pH and sand content increased and soil organic carbon (SOC), bulk density, clay and silt particle contents decreased. Compared to GT-A, microbial biomass carbon (MBC), microbial biomass nitrogen(MBN), and their allocation ratio of GT-D were significantly more by 2.82, 4.30, 5.77 and 7.15 time. The abundances of total PLFAs, bacterial, actinomyces, gram-positive bacteria and gram-negative bacteria increased 106.8%, 117.2%, 74.9%, 107.9% and 207.2%. The raise in ground water level enhanced the environmental stress on the microbial community, resulting in a decrease in microbial bio-diversity. Soil pH, moisture, sand contents as well as the C:N ratio have significant correlations with PLFA signatures. Further, the microbial quotient (MBC/SOC) is mainly influenced by soil pH and texture. In summary, the results show significant effects of ground water level on both soil microbial biomass and community structure during the dry season.