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.