Species diversity is one of the most important characteristics of biological communities and an important factor affecting the function and stability of ecosystems. The variation in diversity has been a topic of great interest in ecological research for many years, whereas β diversity, an important aspect of species diversity, has been studied in terrestrial ecosystems and freshwater ecosystems more than in marine ecosystems. Haizhou Bay is a traditional fishing ground in the Yellow Sea and historically has had rich fishery resources. However, the fishery resources in Haizhou Bay have seriously declined in recent years due to overfishing, environmental pollution, and human activities. The purpose of this study was to understand the temporal and spatial variation in β diversity of the fish species in Haizhou Bay to provide a scientific basis for the conservation of fishery resources and the construction of protected marine areas. The data in this study were collected from fishery resource surveys conducted in Haizhou Bay in the autumn of 2011 and 2013–2019 using bottom trawl. Non-parametric methods, including the Chao’s and Bootstrap approaches, were used to estimate the number of fish species, namely species richness, in the entire area of Haizhou Bay and in each sampling station. On this basis, β diversity was calculated according to the additive principle with a variety of measurement methods, including Sorenson’s index and Cody’s index, which reflects the similarity of species composition between the two groups and the substitutability between groups, respectively. To evaluate the spatial variation in β diversity, survey stations were divided into two groups along the 20 m isobath roughly by K-Means Cluster. The results of this study showed that the richness and β diversity of the fish species in Haizhou Bay decreased significantly in recent years, the Cody’s index decreased, and the Sorenson’s index increased slightly. The result reflected biotic homogenization in the marine ecosystem and it also indicated a remarkable difference in the trend of β diversity between deep water and shallow water. The decline in biodiversity has become a common phenomenon, which is closely related to human activities, especially long-term overfishing. In addition, environmental factors, especially the rise of sea water temperature, also contribute significantly to biotic homogenization. In summary, our research indicated that the abundance and β diversity of the fish species in Haizhou Bay decreased substantially from 2011 to 2019, and these changes were associated with the life history of fish species and their adaptability to the environment. These changes were also closely related to human activities, such as overfishing, environmental pollution, habitat destruction, and the water temperature increase caused by climate change. The driving mechanism remains to be further explored. In-depth studies on β diversity are helpful for understanding the fluctuation of marine fish communities, managing and protecting fishery resources, and providing a reference for constructing marine protected areas, which have great significance to the sustainable use of fishery resources and the protection of biodiversity.