Xiaoheishan Island is located in Bohai Strait and affiliated with Miaodao Archipelago, which lies in Shandong province. The paper identifies the potential area for sustainable restoration of Stichopus japonicas, Scapharca broughtonii and Mytilus edulis in the shallow waters of Xiaoheishan Island using a habitat suitability index model (HSI). Seven screened environmental factors were involved in the HSI model for each species respectively. In summary, the following 9 factors:water temperature, salinity, water depth, pH, sediment composition, dissolved oxygen, organic carbon, current velocity and Chlorophyll a were analyzed in this study. Specific factor piecewise functions have been used to transform environmental factor values into normalized quality indexes (0, 2, 3 and 4). The weight of the each factor was judged with the expert knowledge and the analytic hierarchy process (AHP) method. Thus, the habitat suitable analysis maps were obtained after data interpolate, reclassification and raster calculation with the aid of GIS spatial analysis module. In addition, the analysis of habitat suitability was conducted for four seasons in this paper in order to get more detailed information. First, the results suggest that the entire area was suitable for restoration of S. japonicas and M. edulis, along with no spatial differences but obvious seasonal changes for the 2 species. For S. broughtonii, it is noteworthy that the study area was defined as the suboptimal habitat by the reason of aestivation. Moreover, the northeast region was detected as the optimal site for S. broughtonii propagation, followed by the western part. Meanwhile, the suboptimal habitat accounted for the majority of study area throughout the year with the marginal habitat only appeared in winter. Water temperature was the main factor causing seasonal variation, while sediments composition was remained as the key reason for the differences in habitat sites. Overall, the results indicated the great feasibility for the long-term survival and successful restoration of S. japonicas, S. broughtonii and M. edulis. This study could provide supports and suggestions for subsequent research of biological diversity protection and ecological restoration.