The study aimed to investigate the potential of using Apocyclops royi as a food source for nurturing young Macrobrachium rosenbergii shrimp. Shrimp raised with A. royi showed significant increases in weight gain and growth rate compared to those raised with Artemia. The gene Myostatin in M. rosenbergii shrimp fed with A. royi exhibited a similar amino acid sequence to that of M. nipponense shrimp. Additionally, the expression of the gene ArLGBP increased in shrimp raised with A. royi, while the gene Hsp70 remained unchanged. The study also found an increase in beneficial bacteria and a decrease in harmful bacteria in the gut microbiota of shrimp fed with A. royi. Overall, using A. royi as a food source promoted growth, enhanced immune gene expression, and improved gut microbiota in young M. rosenbergii shrimp.