Pesticide residues in agricultural products and the environment have been studied extensively over the years. Through the excessive or illegal use of pesticides, residues enter the surrounding environment and are absorbed by animals. Livestock and fishery products are subject to pesticide residue regulation, which includes the establishment of maximum residue limits. However, currently, fishery products are regulated only for ethoxyquin, neglecting the potential for bioaccumulation. This study aims to develop a method for the multi-class, multi-residue analysis of pesticide residues in fishery products—flatfish, eel, shrimp, and Manila clam—based on the QuEChERS method. A total of 327 compounds, including 263 pesticides and their metabolites, were identified using liquid chromatography and gas chromatography–tandem mass spectrometry. The method can quantify 263 pesticide residues in flatfish, 265 in eel, 264 in shrimp, and 263 in Manila clam, respectively. Additionally, the method can be applied to quantify 244 pesticide residues in seaweed. The method proves effective and useful for monitoring both food safety and environmental contamination.