A 6-week 5×2 factorial study was conducted to examine the effects of stocking density and feeding frequency on growth performance, body composition, digestive enzyme activity, and tissue histology of juvenile hybrid groupers raised in an indoor circulating water system. Triplicate groups of fish were reared in tanks following a factorial design consisting of ten treatments including 5 stocking densities (SD) [1.1 kg m−3(0.55 kg fish per tank, SD1.1), 2.2 kg m-3(1.1 kg fish per tank, SD2.2), 3.3 kg m−3(1.65 kg fish per tank, SD3.3), 4.4 kg m−3(2.2 kg fish per tank, SD4.4) and 5.5 kg m−3(2.75 kg fish per tank, SD 5.5)] and 2 feeding frequencies (FF) [3 meals a day (FF3) and 2 meals a day (FF2)]. The resulting 10 treatments were G1(SD1.1,FF3), G2(SD2.2,FF3), G3(SD3.3,FF3), G4(SD4.4,FF3), G5(SD5.5,FF3), G6(SD1.1,FF2), G7(SD2.2, FF2), G8(SD3.3, FF2), G9(SD4.4, FF2) andG10 (SD5.5, FF2). Feed consumption and temperature were recorded throughout the experiment. After 6 weeks, the results indicated that the weight gain rate (WGR) and specific growth rate (SGR) of fish in the G7 group were significantly higher than those of other groups (P< 0.05), followed by G1, with G3 being the lowest. Weight gain and specific growth rates were generally higher in fish fed twice a day than those fed three times a day. The variations in protein content between groups were consistent with the muscle protein content trends. Feeding frequency and stocking density had significant effects on serum aspartate aminotransferase (AST), alanine aminotransferase (ALT), triglycerides (TGs), and cholesterol (CHO) (P < 0.05). Regarding immune function, grouper albumin (ALB), serum lysozyme (LZY), superoxide dismutase (SOD), and alkaline phosphatase (AKP) were significantly affected by stocking density and feeding frequency (P< 0.05). Pepsin and lipase activities in the stomach, intestine, and liver were also affected. The histological structure of the stomach, liver, and intestine in G1, G2, G7, and G8 fish was relatively normal, whereas those of the remaining groups exhibited varying degrees of damage. Overall, the optimum stocking densities were 1.343 kg/m3 (approximately 10 fish) and 2.004 kg/m3 (approximately 20-30 fish) when the fish were fed 3 and 2 times per day, respectively.