Exploring the interactions between marine mammals and fisheries is essential for ecosystem-based fisheries management. In recent years, the conservation of fishery resources in the adjacent waters of Zhangzi Island has continuously improved, leading to a gradual increase in the number of cetaceans such as minke whales (Balaenoptera acutorostrata) and finless porpoises (Neophocaena asiaeorientalis sunameri). However, activities such as pelagic trawling and offshore recreational fishing continue to impact the prey resources of these cetaceans. Despite this, the broader ecological interactions between cetaceans and fisheries, particularly their roles in the food web and their impacts on the structure and function of offshore ecosystems, remain unclear. To address this gap, a food web model was developed using Ecopath for the coastal waters adjacent to the Zhangzi Island. This model allowed to assess the ecosystem's structural and functional characteristics, examine the trophic roles of cetaceans, and analyze their interactions with fisheries. The results indicated that trophic levels (TL) within the ecosystem ranged from 1.00 to 4.24, with minke whales at 3.74 and finless porpoises at the highest level (4.24). The keystone index and relative total impact of finless porpoises (−0.53 and 0.33, respectively) was greater in magnitude than those of minke whales (−0.82, 0.17). Mixed trophic impact (MTI) analysis revealed that both the minke whale and finless porpoise exerted greater negative than positive impacts on trophic levels IV and III species. Notably, the finless porpoise showed the strongest negative influence on the food web (7.5%), with particularly pronounced effects on trophic level III species (14.5% positive vs 22.2% negative impacts). Among fishing activities, pelagic trawling (30.8%) and recreational fishing (26.7%) demonstrated the highest negative impacts on the food web. In this ecosystem, cetacean consumption accounted for merely 0.3% of total species consumption, while diving fishing (39.2%) and pelagic trawling (24.5%) dominated the total consumption flows. Furthermore, niche overlap index indicated substantial resource competition between finless porpoises and pelagic trawling (0.75), whereas overlap indices between both cetaceans (minke whale: 0.03; finless porpoise: 0.33) and overall fisheries remained relatively low. Although the finless porpoise exhibited stronger interactions with fisheries, the food web impacts from cetaceans’ predation were significantly lower than those caused by fishery exploitation. These findings provide valuable references for achieving coordinated management of local marine mammal conservation and fishery resources.