Tidal algal reefs are considered high biodiversity habitats but have received little attention. Macrobenthos communities were characterized in a gradient of habitat types on the tidal flats in northwestern Taiwan, including algal reefs (R), mixed algal reefs and gravel (RG), mixed sand and gravel (SG) and sand (S). Both hydrodynamic movement and surface rugosity were highest in R, followed by RG, SG, and S. The faster the movement and the higher the rugosity were, the higher the density and taxon richness of the macrobenthos community. The relatively slower movement and accumulated sand in S likely resulted in stress on organisms, which led to a lower density and taxon richness of the macrobenthos community. Our results suggest that the main factors structuring the macrobenthos community in the diverse habitat types were hydrodynamic movement and surface rugosity.