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In recent years, with the aggravation of environmental pollution, the study of aquatic ecotoxicology has become a hot topic. Some aquatic organisms, such as large fleas, toads, and zebrafish, have been developed and applied as model organisms. They have been increasingly used to study the bioaccumulation and toxicity of environmental pollutants due to the advantages of their small size, easy reproduction, short life cycle, low maintenance cost, and ability to combine genetic, cellular, and whole organism endpoints. This review summarizes the methods of zebrafish, as a model in aquatic ecotoxicology, using its developmental toxicity, biomarkers, genomics, and phenotype analysis to evaluate the toxicity of environmental pollutants, providing a reference value for researchers to select model animals for aquatic ecotoxicology research.