As an emerging global issue in coastal marine ecosystems, eutrophication may lead to profound ecological consequences or disasters. Six locations in Xiangshan Bay were sampled during 2012–2022 along the eutrophication gradient from the innermost bay with the most eutrophication to the outer bay with the least eutrophication. A trait-based method was adopted to explore the ecological effects of eutrophication on macrobenthic communities. The results showed that the community composition is mostly characterized by deposit feeders and predators with small (1–3 cm) and large (> 10 cm) body sizes, classified as indifferent and tolerant species (AMBI ecological groups), deposit feeders and predators (feeding mode), and a preference for a free living lifestyle. The RLQ and fourth-corner analyses further confirmed that there was a negative correlation between the abundance of small macrobenthic organisms (< 1 cm) and nitrate concentration. Phosphorus was a crucial influencing factor for macrobenthic spatial patterns and was strongly affected by the activities of deposit feeders and the decomposition of macrobenthos. Due to mass organic deposition resulting from increased primary production, long-term eutrophication had led to an increase in the proportion of detritus feeders. In addition, the significant negative correlation between the concentration of dissolved oxygen and first-order opportunistic species represented by the polychaete Capitella capitata indicated tolerance to hypoxia. The macrobenthic community in Xiangshan Bay had been negatively affected but maintains considerable stability in functional diversity and functional redundancy under the influence of long-term eutrophication.