The use of herbicides is believed to have an impact on the metabolism, physiology and biochemistry of fish. In this study, we studied the effects of metamifop on the production and metabolism of Monopterus. albus living in the water. According to the semi-lethal concentration of metamifop for 96 h, four MET concentration groups (0.2-, 0.4-, 0.6- and 0.8 mg L−1) were set up for 96 h exposure test. The ammonia discharge rate decreased, hemolymph ammonia content increased significantly, and hemolymph urea nitrogen content decreased at all time periods of metamifop exposure. In liver, the protein content decreased, the neutral protease content increased significantly (p < 0.01), amino acid content increased, and ATP content increased significantly (p < 0.01). In brain, the protein content increased, the activity of acid protease, neutral protease and alkaline protease all decreased, amino acid content decreased significantly (p < 0.01), and the content of ATP decreased. Glutamic-pyruvic transaminase (GPT) activity did not change in liver but decreased in brain. Glutamine synthetase (GS) activity decreased in liver and increased in brain. Glutaminase (GLS) activity decreased in liver and increased in brain. In conclusion, the liver and brain tissues of M. albus react differently to MET exposure. The liver mainly synthesizes energy through hydrolyzed protein, while the brain mainly synthesizes protein. Amino acids produced by protein hydrolysis cannot be converted to alanine for storage, and the degraded amino acids lead to the elevation of endogenous ammonia. MET inhibits the removal of ammonia from M. albus. Only liver tissue can detoxify the eel by converting ammonia into glutamine. Brain should have to tolerate high levels of endogenous ammonia.