Red tilapia (Oreochromis spp.) has been favored by farmers in recent years because of its superior growth performance and competitive market price, but there is a lack of experimental data related to growth and health of red tilapia in land-based aquaculture tanks. In this study, red tilapia (initial weight 27.62 ± 2.43 g) was cultured with three stocking densities (30, 40, or 50 fish/m3, named 30F,40F and 50F) in the culture mode for 60 days, including two feeding frequencies (2 or 3 times/day, named 2 T and 3 T), and various growth and metabolic parameters were assessed along with the intestinal microbiome analysis. The 30 fish/m3 groups achieved the better weigh gain rate and specific growth rate (p < 0.05). The growth rate and condition factor of 40F groups were close to those of 30F groups, the yield of 40F groups were not significantly different from that of 50F groups (p > 0.05), and it had the highest survival rate (p < 0.05). The 3 T groups has a higher growth rate and yield but also has a higher rate of feed conversion (p < 0.05). The 30F groups had higher lipase levels, but a higher fat content in this group, more lipids were observed in the liver, and resulted in higher blood glucose levels (p < 0.05). The 40F groups showed healthier physiological and biochemical indicators, as its total cholesterol, lysozyme and antioxidant enzymes levels were similar to those of the 30F groups (p > 0.05), alkaline phosphatase, amylase and trypsin levels were higher than those of the other groups, and aspartate transaminase levels were the lowest (p < 0.05). The 50F groups had higher cortisol, alanine transaminase and malondialdehyde levels, lower lysozyme and digestive enzyme activities, and blood cell infiltration in the liver (p < 0.05). In terms of different feeding frequencies, the 3 T groups had higher crude protein content, catalase and total superoxide dismutase levels, wider villus width and lower blood glucose level, while the 2 T groups had higher triglyceride, total cholesterol, lysozyme, alkaline phosphatase and some digestive enzymes activities (p < 0.05). From the perspective of intestinal microbiota. The 40F groups had a better intestinal flora, and 40F-3T groups observed a better balance of flora, while 40F-2T groups had more digestion-related flora. Considering the growth rate, health status, and yield, the optimum culture condition was determined to be stocking density of 40 fish/m3, and feedings 3 times/day were recommended. The experiment provided theoretical basis and experimental data for red tilapia culture in land-based aquaculture tank mode.