Normal intestinal flora is widely involved in many functions of the host: nutritional metabolism; maintenance of intestinal microecological balance; regulation of intestinal endocrine function and nerve signal transduction; promotion of intestinal immune system development and maturation; inhibition of pathogenic bacteria growth and colonization, reduction of its invasion to intestinal mucosa, and so on. In recent years, more and more studies have shown that intestinal flora is closely related to the occurrence, development, and treatment of various tumors. It is indicated that recombinant phycoerythrin (RPE) has significant anti-tumor and immunomodulatory effects. However, little is known about the mechanism of the effect of oral (or intragastric) administration of RPE on gut microbiota in tumor-bearing animals. In this study, using high-throughput 16S rDNA sequencing, we examined the response of gut microbiota in H22-bearing mice to dietary RPE supplementation. The results showed that the abundance of beneficial bacteria in the mice intestinal flora decreased and that of the detrimental flora increased after inoculation with tumor cells (H22); following treatment with dietary RPE, the abundance of beneficial bacteria in the intestinal flora significantly increased and that of detrimental bacteria decreased. In this study, for the first time, it was demonstrated that dietary RPE could modulate the gut microbiota of the H22 bearing mice by increasing the abundance of beneficial bacteria and decreasing that of detrimental bacteria among intestinal bacteria, providing evidence for the mechanism by which bioactive proteins affect intestinal nutrition and disease resistance in animals.