The benthos in four bays (Rongcheng Bay, Sanggou Bay, Jinghai Bay and Wuleidao Bay) at 19 sampling locations were investigated by taxonomy and subjected to calculate the species constitutions, components of dominant species, and spatial distribution, biodiversity pattern and stability of macrobenthic community structure ranging from 2006 to 2007. A total of 14 water environmental variables from 19 sampling locations in four bays were analyzed by factor analysis, and spearman correlations of main water environmental variables and parameters of benthos community were also investigated. The results showed that the dominant benthos species was Chaetopoda in Rongcheng Bay, Sanggou Bay and Wuleidao Bay. In autumn and winter the highest proportion is Chaetopoda, while in spring and summer Crustacea and Mollusca accounted for the highest ratio in Wuleidao Bay. The hierarchical clustering, un-weighted pair group method with arithmetic mean (UPGMA), and non-metric multidimensional scaling (NMDS) approaches were used to analyze the pattern of community compositions. There existed two macrobenthos assemblages in the survey bays. In spring and winter, the sampling stations of Jinghai Bay and Wuleidao Bay were clustered, and then the sampling stations of Rongcheng Bay and Sanggou Bay formed an independent cluster. In autumn, two groups were constituted in the survey bays. The group I contained the sampling stations of Rongcheng Bay, Sanggou Bay and Wuleidao Bay, the sampling stations of Wuleidao Bay constituted the group II. Both in Rongcheng Bay and Sanggou Bay the macrobenthic Shannon-Wiener indices were higher. The averages Shannon-Wiener index was lowest in Wuleidao Bay in spring, summer and autumn, and in Jinghai Bay in winter. The Spearman correlation analysis between main environmental variables and parameters of benthos community demonstrated that sampling depth and total alkalinity was significantly positively correlated with Shannon-Wiener indices, and significantly negative correlation was established between water temperature and Shannon-Wiener indices in summer. In autumn, Shannon-Wiener indices were negatively correlated with nitrate. The abundance biomass comparison (ABC) calves and W-statistic were used to analyze the disturbed states. In undisturbed states, the community was supposed to be dominated by k-selected species (slow-growing, large, late maturing), the biomass curve lied above the abundance curve, the W-statistic value was positive. With increasing disturbance, the system was increasingly dominated by r-selected species (fast-growing, small, opportunistic), the biomass curve would lie below the abundance curve, and the W-statistic value was negative. The ABC curve and W-statistic value were generated by PRIMER software (Plymouth Routines in Multivariate Ecological Research). It was found that the abundance curves were above the biomass curve and the W-statistic in Rongcheng Bay was below zero also in spring and winter, which indicated that the present macrobenthic communities were heavily disturbed. All the results demonstrated that benthic communities structure were correlated with sampling depth, total alkalinity and water temperature in the summer, and with nitrate and water temperature in the autumn. There existed significant difference in the habitat water environment factors between Wuleidao Bay and the other three bays, contributing to the difference in benthic community structure between Wuleidao Bay and the other three bays. Eutrophication in Wuleidao Bay had some negative impact on benthic communities. The macrobenthic communities in Rongcheng Bay and Sanggou Bay were interfered perhaps due to the tremendous impact of intensive aquaculture activities on marine ecosystems. It is important to protect the macrobenthic communities by enhancing management of marine aquaculture, strengthening the concept of ecological health of aquaculture, and rational exploration of marine biological resources.