Abstract: The research adopts phospholipid fatty acid analysis to quantify the microbial community structure of sediments from Yunliang River in different water types during different periods. The results show the following aspects: ① the microbial biomass is significantly different in different water-stage while the temperature is the dominant factor; ② in the same period, the nutritional content is positively correlated to the microbial biomass; ③ G+ indiated by 16:0 iso、17:0 anteiso、15:0 iso is the main microbial community that affects the sediments microbial community structure and water-stage fluctuation significantly influences the sediments microbial community structure; ④ Monounsaturated PLFAs/ branched PLFAs could reflect the nutrition status as microorganism would turn the monounsaturated PLFAs to cyclopropyl PLFAs and saturated PLFAs in order to suit the new conditions when C/N increased in sediment; ⑤ c(i15:0)+c(i17:0)/c(a15:0)+c(a17:0) can be used as the indicator of Carbon content in water environment.