Oyster reefs (OR) once dominated coastal estuaries but are now one of the most severely impacted marine habitats on Earth. There is little information available regarding the status of natural OR in China. This study examined the seasonal and temporal changes in the Kumamoto oyster Crassostrea sikamea population and associated benthic macrofaunal communities at the largest intertidal OR (Liyashan) of the China Sea in four field surveys (spring and fall in 2013 and 2018). The oyster densities exhibited no evident seasonal variations in either 2013 or 2018 but showed significant temporal changes and declined by 89.66% in spring and 96.27% in fall between 2013 and 2018. The total densities of benthic macrofaunal communities at the reef area of the OR were significantly higher than those at the degraded oyster habitat (DOH) and dramatically decreased by 80.73% in spring and 64.87% in fall between 2013 and 2018. Nonmetric multidimensional scaling ordination indicated the benthic macrofaunal communities differed significantly between the OR and DOH or among the four sampling periods. Analysis of similarity indicated that the benthic communities at the OR had greater seasonal and temporal changes than did those at the DOH, and that temporal changes in benthic communities were greater than seasonal changes at each habitat. The study concluded that the OR had decreased habitat values as the oyster populations and the benthic macrofaunal communities dramatically declined from 2013 to 2018.