The proliferation of coastal infrastructure in the context of coastal development, urbanization, and global change is inevitably related to the transformation of coastal community structure. For restoration of biodiversity in these human-disturbed coastal ecosystems, it is vital to untangle the community structure and thermal environments, with the consideration of the microhabitat-scale thermal environment variations. In the present study, we measured the species richness, α-diversity (i.e. the species composition of each surface of breakwaters), and β-diversity (i.e. the dissimilarities among macrobenthic communities of different surfaces of breakwater) of macrobenthos on the breakwaters on a tropical shore for understanding the variation of the community structure of macrobenthos; we also monitored the operative temperatures in different surfaces of the breakwaters during the experimental period for investigating the roles of microhabitat thermal environment on the community structure of macrobenthos on the artificial infrastructure. Our results showed that there were higher species richness and abundance in the thermally benign microhabitats. The variations of β-diversity indicated that the community structure underwent dramatic changes in different microhabitats and seasons. The population dynamics of thermal-sensitive species (e.g. Patelloida pygmaea, Cellana toreuma, and Siphonaria japonica) largely contributed to the changes in community structure. Redundancy analysis (RDA) results showed that maximum temperature, temperature predictability (i.e. the degree to which a temperature data point in a time series is influenced by its historical values), and heating rate were important thermal characteristics driving community structure on the artificial infrastructure. These results indicate the heterogeneity of thermal environments among different microhabitats is crucial for maintaining the community structure of macrobenthos on the artificial infrastructure and suggest that structural complexity should be considered for biodiversity conservation in the design and construction of coastal infrastructure.