A 6-week feeding trial was conducted to investigate the effects of adding tributyrin (TB), alone and in combination with fructooligosaccharides (FOS) in high soybean meal (SBM) diets on growth performance, innate immunity and intestinal morphology of shrimp (Litopenaeus vannamei). Six isonitrogenous and isolipidic diets were formulated: positive control diet (PC, containing 250 g/kg fishmeal (FM) and 285 g/ kg SBM), control diet (C, containing 125 g/kg FM and 439.2 g/kg SBM) and four experimental diets with 10 g/kg TB (T1), 10 g/kg TB + 1.0 g/kg FOS (T2), 10 g/kg TB + 2.0 g/kg FOS (T3) and 10 g/kg TB + 4.0 g/kg FOS (T4) supplemented to the control diet. The results showed that shrimps fed diet C had the poorest growth, and no significant differences in growth performance and survival rates were observed in shrimps fed diets PC, T1, T3 and T4. Dietary TB supplementation significantly enhanced hepatopancreas trypsin, haemolymph ACP and AKP activities and also improved mucosal thickness (MT) (p < .05). Compared with supplementation of TB alone, the combination of TB and FOS not only further improved the above indicators but also enhanced the villus height (VH), hepatopancreas lipase and haemolymph SOD activities, while hepatopancreas MDA level decreased significantly (p < .05), especially in groups with higher doses of FOS (2 and 4 g/kg). In conclusion, partial FM replacement with SBM had negative effects on shrimp, and TB alone and in combination with FOS can improve the growth performance, innate immunity and maintain healthy intestinal morphology of shrimps fed with high SBM diets.