Abstract: The fishery resource status in the distribution area of the cetaceans in the South China Sea is crucial for cetacean conservation. In this study, 122 water samples were collected during five cetacean surveys in the South China Sea from 2020 to 2023, during which 18 species of cetaceans were sighted. The environmental DNA metabarcoding focusing on mitochondrial Cytb were performed, and a total of 91 fish species were detected, which belong to 1 class, 11 orders, 38 families, and 75 genera. Among them, 23 species were found in both spring and summer, 19 species were unique to spring, and 49 species were unique to summer. Oxyporhamphus Micropterus （Beloniformes） was the dominant fish species in both seasons. There was a positive correlation between the occurrence of Mesoplodon hotaula and Grampus griseus with Exocoetus monocirrhus （Beloniformes）, which suggested that cetaceans in the South China Sea may feed on Beloniformes fish. The abundance of Encrasicholina punctifer （Engraulidae） was high in the Xisha Archipelago, while the relative abundance of Hilsa kelee （Clupeidae） was high near Weizhou Island, which indicated that cetaceans prefer Clupeidae and Engraulidae fish. However, due to the abundance of Beloniformes in the Xisha Archipelago, they might also be a food source for cetaceans. Therefore, the fishery management in the Xisha Archipelago should focus on monitoring the resources of Beloniformes, Clupeidae, and Engraulidae fish to ensure the food supply for cetaceans and strengthen the protection.