Procambarus clarkii is an important freshwater aquatic species in China, and there are three popular farming models currently: The artificial feed finishing model (AF), the rice-crayfish co-culture aquaculture model (RS), and the wild ecology model (WS). Three extraordinarily different breeding environments have a considerable degree of influence on the growth, development, and health of the host. The structure and function of intestinal microorganisms are closely linked to the host's metabolism, development, physiology and health. To investigate this issue, metagenomic analysis was used to reveal the taxonomic composition and functional diversity of the gut microbiota of P. clarkii.