Abstract: Mussel reefs provide habitats and abundant food sources for marine organisms. This study selected two typical habitats—raft culture areas and natural mussel reefs—at Gouqi Island as study sites, and explored the ecological driving characteristics of different habitats by comparing the community structure, stability, and secondary productivity level of macro-epifauna. Results showed that: (1) Annual mean biomass of macro-epifauna was similar between the two habitats, but the raft culture habitat exhibited a typical “high abundance, low diversity” pattern. Community structures differed significantly between the two habitats (R = 0.919, P = 0.001), with an average dissimilarity of 85.09%. Abundance-Biomass Comparison (ABC) curves indicated that the natural habitat community was relatively stable, whereas the raft culture habitat suffered significant disturbance in summer and autumn. (2) Community structure differences directly drove the differentiation of productivity levels. The natural habitat, dominated by highly calcified Thecostraca, maintained a higher basic carbon stock (218.58 g C/m²) via high biomass; whereas the raft habitat showed “high turnover, high secondary production” characteristics due to the seasonal succession of short-lived species such as Ascidiacea and Malacostraca, with its secondary productivity level (56.84 g C/m²/yr) higher than that of the natural habitat (45.01 g C/m²/yr). (3) Cohesion analysis revealed significant differences in collaboration-competition trade-offs (CnCp) between the two habitats; the natural habitat was driven by intense competition, while the raft habitat showed enhanced collaboration. In conclusion, although the raft mussel habitat was weaker in community stability than natural mussel reefs, it maintained a higher secondary productivity level through the high turnover of epifauna, playing a key role in driving coastal ecosystem energy flow. These findings provide a scientific basis for coastal ecological aquaculture planning and marine biological resource assessment.

Key words: mussel reef, raft aquaculture, macro-epifauna, community structure, secondary productivity