The rapid development of marine aquaculture in China, especially that of raft shellfish culture, not only contributes directly to China’s economic benefits, but also facilitates fishery resources conservation to a certain extend. Large-scale raft culture, in a sense, has played a role of artificial floating reefs, providing temporary or permanent feeding or sheltering habitats for fish, which coincides with the core idea of marine ranch development based on floating reef systems. Fish assemblages and their community characteristics in raft mussel farming habitats play key roles in understanding functions of floating artificial reef system in marine ranching area. Hence, fish composition and community structure in surface and bottom levels of a mussel farming habitat in Gouqi Island waters and an adjacent rocky reef habitat were analyzed based on data collected by multi-mesh trammel nets from September to December 2020. Index of relative importance (IRI), species diversity indices and non-metric multidimensional scaling (nMDS) analysis were used. A total of 55 fish species belonging to 47 genera in 34 families of 10 orders were collected from two habitats. Among which, 37 species were collected from mussel farming habitat, including 29 species from bottom level and 20 species from surface level; 40 species were collected from rocky habitat. In terms of dominant species composition, Lateolabrax maculatus and Mugil cephalus were the typical dominant species in the surface level of mussel farming habitat, while Nibea albiflora and Sebastiscus marmoratus were the typical dominant species in the bottom level of mussel farming habitat. S. marmoratus was also a typical dominant species in the reef habitat. The similarity analysis showed that the similarity in species composition between the surface and bottom level of mussel farming habitat and the reef habitat was below a moderate level of dissimilarity. Diversity analysis showed that the overall diversity of mussel farming habitat was higher than that of rocky reef habitat, but not significantly (P>0.05). The multivariate analysis indicated that fish community could be grouped into three types in the two habitats, though it was not strictly consistent with the surface area, bottom area and reef area. Results of ANOSIM suggest that there was significant difference among grouped communities (P<0.05). Our study suggests the following: ① the presence of large-scale raft culture facilities in rocky island waters attract many pelagic and demersal fishes, providing additional habitat for dominant rocky fishes, among which S. marmoratus, N. albiflora, M. cephalus and L. maculatus could be suitable target species in the marine ranching programs of northern East China Sea; ② mussel farming habitat and nearshore rocky reef habitat have obvious complementary and gain of habitat functions, which play essential roles on protection of common commercial fish populations in the East China Sea and comprehensive conservation of local fish in different life stages. It is hoped that this study may contribute to technology as well as target fish selection in marine ranching programs and the application of artificial habitat construction model carried out in island waters.