BACKGROUND: Microbiota sequencing has emerged a powerful tool for advancing aquatic nutrition research. However, few studies have comprehensively investigated the host microbiota's response to trace minerals. This study examined the role of organic copper supplementation in promoting the health of farmed white shrimp (Penaeus vannamei) from a microbiota perspective. RESULTS: In an 8-week feeding trial, shrimp were fed diets supplemented with no copper, 30 mg/kg inorganic copper (CuSO·5HO) or organic copper (Cu-proteinate). The apparent digestibility coefficients of copper and zinc, along with carbon and nitrogen assimilation, were determined. The V3-V4 region of the 16S rRNA gene was sequenced from feeds, intestines, gills, and water samples. Shrimp that fed the organic copper diet demonstrated healthier physiological status, higher apparent digestibility coefficients of both copper and zinc, as well as greater accumulation of copper, zinc, carbon, and nitrogen. The organic copper group exhibited distinct microbial diversity and a more complex microbial co-occurrence network, characterized by enhanced natural connectivity and robustness. Keystone taxa, including Vibrio, Candidatus_Bacilloplasma, and Photobacterium, contributed to network stability. Taxa associated with nutrient metabolism, including Butyricicoccus, Lactobacillus, and genera in the family Lachnospiraceae, Prevotellaceae, Rikenellaceae and Ruminococcaceae, were significantly enriched, correlating well with improved nutritional profiles. In accordance, functional annotation revealed that the organic copper group exhibited higher abundances of functional modules associated with nutrient and energy metabolism such as carbon and nitrogen cycling. Furthermore, host-selective pressure shaped the unique microbiota composition in the intestine and gill, which differed from the surrounding water and water source, with the gill microbiota potentially serving as a transitional bridge shaping the intestinal microbiota. CONCLUSIONS: More stable host microbiota, enriched nutrient-metabolizing taxa, and enhanced ecological cycling in this study provide a potential strategy for innovative aqua-feed development. Our findings offer novel microbiota-centric insights into the role of organic copper in healthy shrimp farming.