Taurine is an indispensable amino acid for many fish species and taurine supplementation is needed when plant-based diets are used as the primary protein source for these species. However, there is limited information available to understand the physiological or metabolic effects of taurine on fish. In this study, 1H nuclear magnetic resonance (NMR)-based metabolomic analysis was conducted to identify the metabolic profile change in the fish intestine with the aim to assess the effect of dietary taurine supplementation on the physiological and metabolomic variation of fish, and reveal the possible mechanism of taurine’s metabolic effect. Grouper (Epinephelus coioides) were divided into four groups and fed diets containing 0.0%, 0.5%, 1.0%, and 1.5% taurine supplementation for 84 days. After extraction using aqueous and organic solvents, 25 significant taurine-induced metabolic changes were identified. These metabolic changes in grouper intestine were characterized by differences in carbohydrate, amino acid, lipid and nucleotide. The results reflected both the physiological state and growth of the fish, and indicated that taurine supplementation significantly affects the metabolome of fish, improves energy utilization and amino acid uptake, promotes protein, lipid and purine synthesis, and accelerates fish growth.