The study was conducted to evaluate the extruded and pelleting feed production on growth performance, intestinal histology and microbiome analysis of juvenile red swamp crayfish, Procambarus clarkii. Crayfish were fed either pelleted or extruded feeds that were made using the same formula. Crayfish fed extruded feed had a lower feed conversion ratio, as well as significantly higher levels of trypsin and amylase (p < 0.05) than those fed pelleted feed. However, other growth indices and the activity of lipase were not significantly influenced by the feed processing technique (p > 0.05). In comparison with the pelleted feed group, the lamina propria thickness of crayfish fed extruded feed was significantly lower (p < 0.05). Additionally, the abundance of intestinal microbiota in the extruded feed group was higher than that in the pelleted feed group. The dominant phyla in the intestine of both groups were Proteobacteria, Tenericutes, and Firmicutes, and the relative abundance of Proteobacteria in the extruded feed group was significantly higher than that in the pelleted feed group (p < 0.05). These results revealed that P. clarkii fed extruded feed had higher feed utilization and better intestinal health.