<p>Dongshan Island, a typical subtropical island along the southern coast of Fujian Province, China, is surrounded by numerous bays. To explore significant differences in subtidal macrobenthic communities and water quality between semi-enclosed and open bays around Dongshan Island, an investigation was conducted in spring and autumn 2020. Eight macrobenthic community and fourteen water quality parameters were measured across two semi-enclosed bays (Dongshan Bay and Zhao’an Bay) and two open bays (Gongqian Bay and Wujiao Bay). Results showed that six macrobenthic parameters, including species number, density, diversity index (<i>H</i>′), richness index (<i>d</i>), AZTI marine biotic index (AMBI), and multivariate AMBI (M-AMBI), and two water quality parameters (water depth and salinity) in the semi-enclosed bays were significantly lower than those in the open bays. In contrast, eleven water quality parameters, including pH, suspended solids (SS), dissolved oxygen (DO), inorganic nitrogen (IN), oils, Cu, Zn, Pb, Hg, Cd, and As in the semi-enclosed bay were significantly higher than those in the open bay. Cluster analysis, nMDS analysis, and relative importance indices (<i>IRI</i>) consistently confirmed distinct macrobenthic community compositions between semi-enclosed and open bays. BIO-ENV analyses indicated that water depth, water temperature, salinity, IN and As were the main factors shaping the subtidal macrobenthic communities around Dongshan Island. In conclusion, geographical characteristics (semi-enclosed bay and open bay), combined with marine aquaculture activities, freshwater inflow, and sea wall construction, contribute to lower macrobenthic diversity and poorer water environmental quality in semi-enclosed bay compared to open bay.</p>