The coastal marine area of northern Zhejiang (East China Sea) is important to regional development in the southeast of China. Marine sediment prokaryotes play crucial roles in regional biogeochemical cycling. However, the sediment prokaryotic community assembly and metabolic potential in this ecosystem had not been revealed on an extended spatial scale. We collected surface sediment samples across sixe typical zones (Yushan, Xiangshan Harbor, Hangzhou Bay, eastern Zhoushan Islands, eastern Xiangshan, and Sanmen Bay) of this area and combine 16S rRNA gene sequencing, community-level metabolic reconstruction, and sediment physicochemical measurement to investigate the variations in taxonomic composition and metabolic gene family composition with geography and related environmental conditions. Geographic distance effect won the arm-race in shaping beta-diversity pattern with the major environmental drivers such as oil, temperature, texture, sulfide, and water depth, but left larger proportion of unexplained variation, suggesting the effects of unmeasured factors and stochastic process. We found discriminant assemblages across the zones, suggesting some provincial distributions of prokaryotes. On the other hand, the predicted metabolic potential structure slightly but significantly shifts with geography. The key roles of sulfide and oil in shaping metabolic potential structure suggested the importance of sulfur (S) metabolism in biogeochemical cycling here. Particularly, we found that sulfate reduction was the dominant pathway in S-metabolism in the Yushan sediments as indicated by the evidences from taxonomic composition, predicted enzyme-level gene, and metabolic product. This study provides the first insight into the regional turnover of sediment prokaryotic diversity and metabolic potential in this ecosystem.