Macrobenthos plays an important role in the balance and stability of the ecosystem and is an important indicator of ecological environmental changes. The niche and interspecific associations of dominant macrobenthic species in mussel culture area are rarely reported, making it difficult to effectively determine the effects of shellfish culture on the interspecific relationships of macrobenthic communities and their utilization of environmental resources. To explore the ecological characteristics and resource utilization of the macrobenthos community structure in mussel culture area, we used macrobenthos survey data from a mussel culture area on Shengsi Gouqi Island in spring (April) and autumn (November) of 2021. We then used niche width, niche overlap, association coefficient, and redundancy analyses to investigate the spatial and temporal niches and interspecific associations of dominant species and determine the main environmental factors that affect dominant macrobenthic species distribution. The results showed that 132 macrobenthos species were identified within the study area, with 13 dominant species, including Sternaspis scutate, Amphiura koreae, and Chaetozone setosa. The niche breadth ranged from 1.065 to 2.507, among which the niche width of S. scutate was the highest. The overlapping range of various pairs of niche overlaps was determined to be 0–0.83. The species pairs with the highest overlap values are Chaetozone setosa and Cirratulus filiformis. Contrastingly, Terebellides stroemii vs Chaetozone setosa, Prionospio queenslandica, and Cirratulus filiformis, Kuwaita heteropoda vs Glycera rouxii had the smallest ecological niche overlap. The variance ratio method demonstrated that the dominant macrobenthos species showed no significant negative association. Chi-square tests and association coefficients also showed that most species pairs were not significantly associated. Redundancy analysis indicated that dissolved oxygen, water temperature, and sediment median particle size were the main environmental factors affecting the distribution of dominant macrobenthic species at this mussel culture site on Gouqi Island. Polychaetes were the main macrobenthic niche species in this mussel culture area, followed by Ophiuroidea species. Niche overlap was generally in a low-level state, the dominant species primarily exhibited an insignificant negative association, and the niche of each dominant species was relatively independent. Throughout this study, we can clearly establish the status and role of the dominant species in the community and the relationship between these species. The results showed that the resource dimension of the study area was higher and the competition for resources among the dominant species was small. The results of this study provide a reference for future evaluation of the ecological effects of mussel culture activities and the management of culture capacity.