In Qidong, Jiangsu Province, there used to be 440 km² of mudflats, which is a crucial habitat for benthic shellfish—a significant and unique marine resource. However, human activities such as mudflat reclamation and coastal construction have reduced the suitable habitat for shellfish and altered the local ecological factors. Conversely, shellfish proliferation and release activities have also been performed frequently, which have impacted the resources, biodiversity, and overall equilibrium of benthic shellfish ecosystems. Presently, the lack of understanding regarding the distribution and community structure of shellfish resources has hindered the effective management of shellfish and the protection of germplasm resources. Conversely, there have been frequent shellfish proliferation and release initiatives. Here, we aimed to systematically understand the biodiversity and resource status of benthic shellfish, explore the main environmental factors affecting the community structure, and provide basic data for the shellfish resources protection and habitat restoration. For this, we surveyed 8 sections of Qidong intertidal mudflats in the spring and autumn of 2019 and analyzed the species composition, diversity, density, dominant species, and distribution of shellfish. A total of 30 species of benthic shellfish were recorded during the spring and autumn surveys, including 14 species of gastropods and 16 species of bivalves. Across the elevation gradient of the intertidal zone, the average density of benthic shellfish exhibited the following trend: high tide zone＞medium tide zone＞low tide zone. The dominant species of benthic shellfish in intertidal mudflats were Mactra veneriformis, Dosinia laminata, Meretrix meretrix, Moerella iridescens, and Bullacta exarate. The results of non-metric multidimensional scaling showed that the benthic shellfish could be divided into three groups. The first group comprised three tidal zones of the Q1 section (Lvsi harbour) housing M. iridescent and R. philippinarum; the second group included the three tidal zones of Q8 section (Qixingsha) and several middle and low tidal zones of central sections, with D. laminata and B. exarate being the predominant species. The remaining central sections formed the third group, with M. meretrix and M. veneriformis as the characteristic species. Canonical correlation analysis showed that the densities of both M. meretrix and M. veneriformis were positively correlated with sand content and D50, while being negatively correlated with clay content. The density of M. iridescens was positively correlated with clay content, while being negatively correlated with sand content. D. laminate was negatively correlated with total organic carbon. A clear differentiation was observed in shellfish composition in Qidong intertidal mudflats, owing to the significant differences in salinity and bottom plasmid diameter. Our results suggest that the northern mudflats must be developed into protection areas for small shellfish resources (such as M. iridescens and R. philippinarum). In contrast, the central coastal mudflat is suitable for large bivalve shellfish (such as M. veneriformis and M. meretrix). Sandbars are not conducive to the development of shellfish since they are susceptible to various factors such as channel fluctuations, strong tides, typhoons, and storm surges.