Biofouling refers to the phenomenon where fouling organisms attach to and accumulate on artificial surfaces, adversely impacting human production activities. In recent years, the economic losses caused by biofouling have accounted for a substantial portion of the production costs in China’s mariculture industry. However, current control technologies remain inadequate, highlighting the urgent need to develop green and sustainable control strategies tailored to marine aquaculture environment. Using trophic cascade effects to control fouling organisms has become a focal point of recent research. This approach enables the selection of different biological agents based on the specific environmental characteristics of a given marine area, achieving effective control of fouling organisms while also providing certain economic benefits. This study focused on the selection of representative fish species including Siganus canaliculatus, Sparus latus, Rhabdosargus sarba, and Triacanthus biaculeatus, from the Dongshan Bay region of the Fujian Province, to evaluate their potential as ecological controllers of biofouling in Dongshan Bay. High-throughput sequencing technology was used to analyze the 18S rDNA gene sequences within the digestive tracts of these four fish species to elucidate their dietary composition and assess the differences in their consumption of fouling organisms. The results indicated significant differences in the dietary composition of the four fish species. Triacanthus biaculeatus predominantly consumed osteichthyes, displaying a strong carnivorous preference, while Siganus canaliculatus, Sparus latus, and Rhabdosargus sarba exhibited omnivorous feeding habits. Notably, Sparus latus showed a preference for herbivorous diet, while Rhabdosargus sarba tended towards carnivorous prey. Of particular interest is the finding that Siganus canaliculatus demonstrated an obvious preference for consuming fouling organisms, particularly ascidians, as a major component of its diet. Furthermore, the study revealed that larger individuals of Siganus canaliculatus [(180±2) mm] consumed a greater quantity and variety of ascidians than smaller individuals [(120±2) mm]. This study highlights the potential application of Siganus canaliculatus in the ecological control of biofouling, providing new scientific insights and theoretical support for the development of ecological biofouling control strategies and methods.