Coral reef ecosystems have great economic, social, and ecological value. The ecological success of coral reef ecosystems critically depends on coral-algal symbiosis and coral-prokaryotic partnership. However, seasonal changes underlying these relationships in subtropical hard corals of Hong Kong are poorly studied. Here, we compared the community changes of algal symbionts and prokaryotic partners in Platygyra carnosa and Galaxea fascicularis from Hong Kong collected at two seasonal time points of winter and summer via massively parallel sequencing of genetic markers and multivariate analysis. The results indicated that algal symbionts showed no significant changes between the two seasonal time points but prokaryotic partners changed substantially. Prokaryotic partners putatively involved in photosynthesis, nitrogen fixation, and sulfur oxidation increased significantly from winter to summer, while prokaryotic partners potentially associated with chemosynthesis, ammonia oxidation, and nitrite oxidation decreased significantly from winter to summer. Dissolved oxygen and pH served as the main contributors influencing prokaryotic partners in winter, while temperature, turbidity, and salinity played a dominant role in shaping prokaryotic partners in summer. The findings of the present study suggest that season structures prokaryotic partners but not algal symbionts in subtropical hard corals.