Objectives The meat nutritional qualities of Cyprinus multitaeniata under different breeding environments were studied to provide reference for the healthy and efficient farming and breeding of Cyprinus multitaeniata. Methods The general nutrient composition, amino acids, and fatty acids of the meats from three populations of Cyprinus multitaeniata farmed in Wuming District (WM) of Nanning City, Lingshan County 1 (LS1) and Lingshan County 2 (LS2) of Qinzhou City, Guangxi Province, were measured and analyzed. The nutritional value was evaluated. Results According to the amino acid score (AAS) and chemical score (CS) criteria, the first limiting amino acid of fish meat in all three populations was Met+Cys. The AAS score, CS score, and index of amino acid (EAAI) of each essential amino acid in the LS2 population was the highest, followed by the LS1 population, and the WM population was the lowest. 25 fatty acids were detected in fish meat from all 3 population. The content of ΣPUFA in the LS1 population (23.34%) was significantly higher than that in the LS2 population (19.92%), and the content of EPA+DHA in the WM population (4.26%) was significantly higher than that in the LS2 population. Conclusions The fish meats from the three breeding farms are rich in nutrients and can serve as a supplement of protein with high-quality for the human body. The nutritional value of amino acids in meat in the LS2 population is superior to the other two populations, while the nutritional value of essential fatty acids in meat in the LS1 population is superior to that in the LS2 population.