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An 8‐week feeding trial was conducted to evaluate the effects of dietary nucleotide (NT)‐rich yeast supplementation on growth, innate immunity and intestinal morphology in Pacific white shrimp (Litopenaeus vannamei). Four isonitrogenous and isolipidic practical diets were formulated to contain 0 (control), 10, 30 and 50 g/kg of NT‐rich yeast, respectively. A total of 480 shrimp with an average initial body weight of 1.86 ± 0.02 g were randomly allocated into four groups, with four replicates per group and 30 shrimp each replicate. The results indicated that shrimp fed the diet containing 50 g/kg NT‐rich yeast had significantly higher weight gain (WG), specific growth rate (SGR) and protein efficiency ratio (PER) than those fed the control diet, and the lowest feed conversion ratio (FCR) was observed in the shrimp fed the 50 g/kg NT‐rich yeast supplemental diet. However, there was no significant difference in survival among all treatments. The crude protein of whole shrimp in the 50 g/kg NT‐rich yeast group was higher than that in the control group. Total protein, triglyceride concentrations, the activities of aspartate aminotransferase and alanine aminotransferase in serum were significantly influenced by the dietary NT‐rich yeast supplementation. The activities of serum phenoloxidase (PO) and lysozyme (LZM) of shrimp fed the diet containing 50 g/kg NT‐rich yeast were higher than those in shrimp fed the other diets. Relative expressions of alp and lzm significantly upregulated in the 30 g/kg NT‐rich yeast group compared to the control group. The intestinal fold height and fold width in the 30 g/kg NT‐rich yeast group were significantly higher than those fed the control diet; and the highest microvillus height occurred in the shrimp fed the 50 g/kg NT‐rich yeast diet. In summary, dietary 30–50 g/kg NT‐rich yeast supplementation promotes growth performance, enhances innate immunity and improves intestinal morphology of Litopenaeus vannamei.