The sulphur amino acids methionine and cysteine and their derivative taurine are metabolically active molecules with interlinked roles in nutritional requirements. Deficiencies in these nutrients are linked to poor growth and health; however, the impacts of these deficiencies on organ structure and function are largely unknown. This study examined the effects of dietary methionine, cysteine, and taurine fed at different levels on yellowtail kingfish liver histology and surface colour, plasma biochemistry, and posterior intestine histology. Samples were collected from two dose-response feeding trials that quantified (1) the taurine requirement and sparing effect of methionine by feeding yellowtail kingfish diets containing one of seven levels of taurine at one of two levels of methionine, and (2) the methionine requirement and sparing effect of cysteine by feeding yellowtail kingfish diets containing one of five levels of methionine at one of two levels of cysteine. Yellowtail kingfish fed inadequate levels of dietary methionine, cysteine, and taurine exhibited thicker bile ducts, less red livers, more intestinal acidic goblet cell mucus and supranuclear vacuoles, and less posterior intestinal absorptive surface area. Further, thicker bile ducts correlated with less red livers (a*, R), whereas increased hepatic fat correlated with a liver yellowing (b*). Our results indicate a shift toward histological properties and functions indicative of improved intrahepatic biliary condition, posterior intestinal nutrient absorption and homeostasis of yellowtail kingfish fed adequate amounts of methionine, cysteine, and taurine. These findings may assist in formulating aquafeed for optimized gastrointestinal and liver functions and maintaining good health in yellowtail kingfish.