In order to better understand the important role of sediment microorganisms in material cycle and energy flow of aquaculture pond system,three shrimp(Litopenaeus vannamei)ponds covered with plastic sheet in the bottom in Hengshan,Ningbo were chosen and phospholipid fatty acid(PLFA)analysis methods were used to investigate the sediment microbial community structure and its relationship with physical-chemical factors during a three-month period(from June to September,2010).The results showed that the sediment PLFAs were mainly contributed by the saturated fatty acid,branched fatty acid and monounsaturated fatty acid; the amount of polyunsaturated fatty acid and cyclopropane fatty acid was relatively smaller.The total microbial biomass,bacterial biomass and fungi biomass increased significantly with culture time.The principal component analysis(PCA)of the characteristic PLFAs in different periods showed the total of PC1 and PC2 explained the composition of sediment microbial community structure of 81.4%.Although the majority of microorganisms in the sediment were bacteria,bacteria/fungi ratio decreased significantly with culture time due to the better adaptation of fungi to the sediment habitat.The ratios of G /G^- bacteria in the later culture period were smaller compared to the mid-period,but did not change obviously from later period to final-period.Redundancy analysis(RDA)showed that the total microbial biomass,bacterial biomass and fungi biomass were significantly correlated with the total nitrogen and G bacterium biomass, G^- bacterium biomass were significantly correlated with the NO₂-N,NO₃-N. All of them were negatively correlated with the secchi depth(SD).The experimental results indicated that throughout the whole culture process,environmental factors of this new model ponds showed good consistency and stability.Simultaneously,the diversity of the sediment microbial community and the coordination between the structure variation and the environment are also relatively reasonable.The results also demonstrated that the PLFA technique well explained the microbial community according to the variation of PLFAs’ composition in different periods,and overcame the shortcomings of traditional culturing analyzing methods to a certain extent.