The successful construction of marine protected areas (MPAs) in temperate waters largely depends on our understanding of the distribution and coexistence of organisms with varying habitat preferences, which helps us to better understand the community patterns mediated by connectivity in coastal areas. This study was conducted to examine the connectivity of nekton assemblages in artificial reefs and adjacent waters, which included five habitats: the artificial reef area (AR), aquaculture area (AA), natural area (NA), estuary area (EA) and comprehensive effect area (CEA), in Haizhou Bay in October 2020. Analysis of variance (ANOVA) showed that there were significant differences in the characteristics and abundances of nekton in each habitat (P<0.05). Approximately 38.2% of the individuals were found in at least three habitats, and very few species were present in only a single habitat. Several highly abundant nekton species were selected according to the kernel density estimates (KDEs), and their body lengths varied gradationally among habitats, potentially indicating migration and diffusion during their life history. The results showed that artificial reefs and adjacent waters in Haizhou Bay are related by similar nekton assemblages and ontogenetic variation. Finally, this study has implications for the conservation and monitoring of nekton assemblages in artificial reefs and adjacent waters, highlighting that the principle of connectivity should be taken into consideration in the design of MPAs and MPA networks that can be applied in different stages of implementation and in different combinations of scenarios.