The physicochemical characteristics, nutritions and the microbial community diversity of sediment core samples of three different space locations in the Lake Taihu were studied by fumigation-digestion and PCR-DGGE analysis respectively. The results indicated that below the surface of sediments Eh declined rapidly with increase of sediment depth and it was under anaerobic condition except the top layer of sediment. pH value changed silightly in the profile of sediments, which ranged from 7.2 to 7.8. TN and TP concentrations in sediments of Lake Taihu were high,and the maximum concentrations reached 2.436 mg/g and 0.731 mg/g, respectively. Their vertical profiles showed that TN and TP concentrations in surface sediments were much higher than in deeper layers and decreased with the increase of the depth of sediment layers. OM concentrations declined rapidly at the top 15 cm of sediment layers. There were prominent difference spatially in microbial diversity and the comparability and dynamics of community structure between different sediment samples of different space locations and different depth. The little significant correlation at alpha < or = 0.05 level was observed between the Eh, pH, percentage organic matter, TN concentration and TP concentration and microbial community structure diversity index except of TN concentration and percentage organic matter.