Spatio-temporal pattern in fish community structure is an important topic for fish community ecologists. In order to better understand fish community characteristics in rocky reef habitats (RR) of the Ma'an Archipelago, we analyzed monthly data from 21 randomly selected sites sampled with multi-mesh trammel nets in 2009. This study reveals spatial and temporal variation in fish community composition, and specifically focuses on seasonal variation in the relative population density of dominant fishes, species richness and diversity, fish community composition, disturbance-related fish community dynamics, and regional differences in fish community patterns based on these indices. Regional differences can be explained by gradients in water turbidity and salinity along tidal currents, so sites set in the southeast were allocated to area A, and sites set in the northwest were allocated to area B. We test the assumption that fish communities in RR habitat within the study area are a function not only of seasonal variations, but also of spatial differences between areas A and B. We use indices of abundance catch per unit effort (A-CPUE) to specify relative population density and community abundance density. Multivariate analysis such as multidimensional scaling (MDS), similarity percentage (SIMPER), analysis of similarity (ANOSIM) and abundance biomass curves (ABC) were introduced to explain spatial differences and temporal variation in fish community composition. Seasonaly migrating species such as Thrissa mystax and Stephanolepis cirrhifer were collected only in summer and autumn, and habitat use by both differs between areas A and B. Larimichthys polyactis and Nibea albiflora can be found in RR habitat all year, but they choose different microhabitats in different seasons. Sebastiscus marmoratus, Agrammus agrammus and Hexagrammos otakii reach their highest population density during late spring and early summer, but they can be found most months in areas A and B, though their densities are time-and space-dependent. The estuarine fish Lateolabrax maculatus appears frequently during autumn and winter but is less abundant in other seasons. SIMPER, ANOSIM and MDS analyses reveal obvious seasonal variations in fish community composition and significant spatial differences between areas A and B (P < 0.001). The population rise and fall of the local species mixed with the immigration and emigration of migrating species both contribute to this pattern. The ABC analysis further indicates that the most stable communities can be found in summer, while the opposite is true in winter. Much more disturbance exists in area A compared to area B during each of the four seasons. We conclude that abundant eco-types and obvious seasonal variations in population density of dominant fishes, which relates to habitat use tendency, contribute together to the spatio-temporal patterns of fish communities in the RR habitat of the Ma'an archipelago. A comprehensive understanding of this is vital to the protection and sustainable use of living resources in the study area.