We surveyed the changes of macro-benthos community composition and nutrients concentration in water in Zhushan Bay after it had been dredged 6 months, which aimed to remove the polluted surface sediments. The results showed that the main benthos in the dredged and un-dredged sediments were Limodrilus hoffmeisteri, Pelopia and Bellamya aeruginosa; compared to the un-dredged sediments, the bio-diversity of dredged areas became lower. However, its biomass became higher than that in un-dredged areas. Concentration range changes of TN and TP in overlying water was 1.64-4.45 mg/L and 0.133-0.258 mg/L, respectively. The post-dredged sediments were still in a higher state of nutrients for the higher concentration nutrients in overlying water, macro-benthos were the species that lived in a serious polluted water environment. Using Shannon-Weaver, Simpson, and Goodnight benthic index to evaluate the results show that the dredged area is in the moderately polluted level, but un-dredged area is in the middle-heavily polluted level. According to the benthos fauna surveys and water quality monitoring results, the effective of sediment dredging could play its role only the strict control on the external pollution resources have been made and reduces the effects of polluted water on the sediments.