The objective of this study was to investigate the effects of organic manganese (Mn) on the health status of white shrimp (Penaeus vannamei ) and the potential correlations between intestinal microbiota and host health, meat quality, and mineral interactions. An 8-week experiment was designed with 7 dietary treatments: C0 , no Mn supplementation; S20, 20 mg/kg Mn from MnSO4·H2 O (inorganic); SO, 10 mg/kg inorganic Mn and 5 mg/kg Mn from Mn-proteinate (organic ); O10 , O20 , O30 and O40 , 10, 20, 30 and 40 mg/kg organic Mn, respectively. The 840 shrimp (approximately 5.30 g) were randomly allocated into 21 tanks, with each diet group containing 3 tanks and each tank accommodating 40 shrimp. The results showed that 10 mg/kg organic Mn supplementation is optimal to replace 20 mg/kg inorganic Mn. Compared with inorganic Mn, organic Mn shaped healthier intestinal microbiota communities and enhanced the competitive advantage of shrimp for Mn uptake, which resulted in promoting nutrition metabolism (higher apparent digestibility coefficient (ADC) of crude protein (P = 0.031) and concentrations of glucose (P = 0.013), triglyceride (P < 0.01) and total cholesterol (P < 0.001)), enhancing antioxidant capacity and immune response (P < 0.05), improving meat quality (P < 0.05), and regulating iron content in whole body and muscle, zinc content in muscle and ADC of copper and zinc (P < 0.01). Pearson’s correlations were observed between gene expression analysis of the immune response and antioxidant capacity, Crude proteinADC, meat texture, and dietary organic Mn , between ADC of copper and zinc, muscle content of iron and zinc (r = 0.55, 0.79, 0.93, -0.91, -0.90, respectively, P < 0.001). In conclusion, organic Mn affects shrimp health status, meat quality and mineral interactions which correlate with changes of the intestinal microbiota.