We report the effects of protein from different duck products on the intestinal flora and physiology of rats. After 30 days of feeding, rats fed water-boiled salted duck protein had the lowest gut microbial diversity and richness. Allobaculum, Lactobacillus, Coprococcus and Eubacterium increased in rats fed wine-cured duck protein, while rats fed water-boiled salted and wine-cured duck protein showed increased serum urea (UREA) concentrations and serum cholesterol (CHOL) to HDL-cholesterol (HDLC) ratios, but decreased retroperitoneal white adipose tissue (rWAT) and perirenal white adipose tissue (pWAT) to body weight ratios. The changes in gut bacteria were mainly associated with the fat-mass index (weight of rWAT or pWAT to body weight ratio), accompanied by the opposite correlation with UREA content. SIGNIFICANCE: It showed that protein from different duck products impacted the intestinal flora and caused physiological changes in rats. Different sources of processed protein vary in their digestibility and digestive kinetics, all of which can affect the intestinal microbiota and physiology. We report the effects is an effort to map the complex interactions of "host physiology-nutrition-microbiota" in order to provide some insights into that food processing can be improved to promote beneficial gut microbes and enhance human health.