Fish and macroinvertebrates (FM) were sampled using multi\|mesh trammel nets from three different habitats including artificial reef (AR), soft\|bottom (SB) and rocky reef (RR) habitats in Sanheng waters during January to August of 2009, in order to study ecological effects of artificial reef habitat on the FM community structure. We compared species composition, dominant species, species diversity and relationship between FM community and environmental variables among the three habitats using multivariate statistics methods and various indices such as species richness, species diversity, IRI, and species evenness indices. A total of 90 species were identified, of which 66 species of fish and macroinvertebrates were collected in the Sanheng AR habitat, which is over 2 times as many as those collected in the SB habitat (32 species) and 6 more species found than the RR habitats (60 species). Species released from stocking programs such as Larimichthys crocea and Sepiella maindroni have only been caught in the AR habitat, indicating that the AR habitat is suitable for released migrating species. As to dominant species, not only SB habitat species like Cynoglossus abbreviates and Platycephalus indicus, but also RR species such as Sebastiscus marmoratus and Hexagrammos otakii, have been found in the AR habitat, suggesting that it is effective in attracting more dominant species from natural habitats. Species richness found in the AR habitat was significantly higher than that found in the other two natural habitats (P＜0.05) and species diversity of the AR habitat was significantly higher than that for the SB habitat (P＜0.05). However, no significant difference was found between the AR habitat and RR habitat in species diversity (P＞0.05). Cluster and MDS analyses indicate that 3 groups of FM assemblages can be divided from the three habitats from January to August, including natural coastal community in January dominated by Lophionus setigerus, rocky community in the AR and RR habitats from February to June, and summer community in all the three habitats dominated by anchovies. Although there was no difference in diversity level and cluster analysis result between the AR and RR habitats, both of them were different from the SB community structure. They were two quite different habitats with different FM community structures according to their low Jaccard similarity values (under 0.4) and different dominant species compositions in each month. BIOENV analysis revealed that an environmental variable, such as temperature, had different effects in deciding values of relative coefficient between FM community and environment in different habitats. The key factor was temperature in the AR habitat, Chl\|a in the SB habitat and both temperature and salinity in RR habitat. We conclude that unique FM community structure had been formed in the AR habitat of Sanheng Isle, which potentially offers a new sanctuary for more native and pelagic species. Construction of artificial habitat is a suitable solution to the conservation of rocky reef resources, and can play an important role in developing marine ranching program.