This study was conducted in three different tidal levels within the intertidal zone of Xunpu, Quanzhou Bay, namely a sandy flat (on high-tide level), a Spartina alterniflora-dominated flat (on middle-tide flat) and an oyster-dominated flat (on middle-tide flat). Investigations were repeated four times between 2011 and 2012. We aimed to understand the spatial and temporal variation of macrobenthic community structure and to evaluate differences among three habitats in the study area. A total of 85 macrobenthic species were recorded, including 39 annelida (38 polychaeta and 1 oligochaeta), 21 crustacea, 20 mollusca (6 gastropoda and 14 bivalvia), 1 cnidaria, platyhelminthes, nemertea, sipuncula and chordata. The results of MDS analysis showed different macrobenthic communities among the three sites in spring and winter, while communities at the S. alterniflora-dominated and oyster-dominated flats were similar in summer and autumn. Within each season, the species number in the S. alterniflora-dominated flat was higher than that at the other two sites, probably due to a mixed sediment type and the shadowing of S. alterniflora acting as a shelter to animals. Instead, density and biomass of macrobenthos were higher at the two middle-tide flats than at the high-tidal flat. The temporal variation of macrobenthos was largest in the high-tidal flat and least in the S. alterniflora-dominated flat. With reduced tidal layer, density and biomass increased.Analysis of two-way ANOVA showed that in the three different habitats the species number, density, biodiversity, evenness and richness of macrobenthos were significantly different, while biomass was not. This because the species number and density were lower at the high-tide flat, dominated by the crab Uca arcuata, than at the other two sites, dominated by the polychaete Mediomastus californiensis. A comparison between different seasons showed that there were significant differences in species number, density, biomass and richness index, while diversity index and evenness index were not. This because the species number on the high-tide sandflat was low, but distribution was more even. The results indicate that larger tidal ranges and longer submerged time in summer and autumn cause more similarity of macrobenthic communities in the S. alterniflora-dominated and oyster-dominated flats. Overall, tidal level, sediment particle size and habitat type were the main factors affecting the temporal and spatial distribution of macrobenthos in Xunpu intertidal zone, Quanzhou Bay.