The aim of the present study was to evaluate the possible effects of inbreeding on the carbohydrate metabolism of Portunus trituberculatus juveniles from different inbred families by measuring the activities of carbohydrate metabolism-related enzymes and glycogen content. The results show that inbreeding weakens the activities of hexokinase in the hepatopancreas and muscle; pyruvate kinase, muscles and serum; and lactate dehydrogenase, gills, but enhances the activity of succinate dehydrogenase in the muscles and gills. The real-time PCR results indicated that the relative mRNA expression levels of the metabolism-related genes decreased as the inbreeding generations increased. The results illustrate that inbreeding gradually reduces carbohydrate metabolism in P. trituberculatus.