Co-occurrence pattern of fish species plays an important role in understanding the spatio-temporal structure and the stability of fish community. Species coexistence may vary with time and space. The co-occurrence patterns of fish species were examined using the C-score under fixed-fixed null model for fish communities in spring and autumn over different years in the Haizhou Bay, China. The results showed that fish assemblages in the whole bay had non-random patterns in spring and autumn over different years. However, the fish co-occurrence patterns were different for the northern and southern fish assemblages in spring and autumn. The northern fish assemblage showed structured pattern, whereas the southern assemblage were randomly assembled in spring. The co-occurrence patterns of fish communities were relatively stable over different years, and the number of significant species pairs in northern assemblage was more than that in the southern assemblage. Environmental heterogeneity played an important role in determining the distributions of fish species that formed significant species pairs, which might affect the co-occurrence patterns of northern and southern assemblages further in the Haizhou Bay.