The distribution characteristic and correlation of AVS and SEM were studied in 28 surface sediments of whole Lake Taihu. The results showed that the concentration of AVS varied greatly in space (COV up to 100.77%), and high concentration of AVS were recorded in estuary of lake. Combined with the distribution characteristic of AVS, deposition rate and load of SO₄^2- probably caused the spatial difference of AVS. The high concentration of SEM was recorded in the area of estuary, and the concentration of SEM in northern part of Lake Taihu was higher than in the southern part. Three models including SEM/AVS, SEM-AVS and SEM-AVS/fOC (Toxicity was predicated when SEM/AVS>9 or SEM-AVS>2 or SEM-AVS/fOC >150μmol/g(OC)) were used to assess the sediment quality of Lake Taihu, and results showed that only site 0^# and 6^# exceeded the threshold of one and two of the three models. Overall, the surface sediments of Lake Taihu could not cause toxicity to benthic organism except site 0^# and 6^#.