Understanding the connectivity of fish among different typical habitats is important for conducting ecosystem-based management, particularly when designing marine protected areas (MPA) or setting MPA networks. To clarify of connectivity among mangrove, seagrass beds, and coral reef habitats in Wenchang, Hainan Province, China, the fish community structure was studied in wet and dry seasons of 2018. Gill nets were placed across the three habitat types, and the number of species, individuals, and body size of individual fish were recorded. In total, 3815 individuals belonging to 154 species of 57 families were collected. The highest number of individuals and species was documented in mangroves (117 species, 2623 individuals), followed by coral reefs (61 species, 438 individuals) and seagrass beds (46 species, 754 individuals). The similarity tests revealed highly significant differences among the three habitats. Approximately 23.4％ species used two habitats and 11.0％ species used three habitats. A significant difference (p<0.05) in habitat use among eight species (Mugil cephalus, Gerres oblongus, Siganus fuscescens, Terapon jarbua, Sillago maculata, Upeneus tragula, Lutjanus russellii, and Monacanthus chinensis) was detected, with a clear ontogenetic shift in habitat use from mangrove or seagrass beds to coral reefs. The similarity indices suggested that fish assemblages can be divided into three large groups namely coral, seagrass, and mangrove habitat types. This study demonstrated that connectivity exists between mangrove–seagrass–coral reef continuum in Wenchang area; therefore, we recommend that fish connectivity should be considered when designing MPAs or MPA network where possible.