〔Abstract〕 Objective This experiment was carried out to study the effects of chronic inflammatory pain on the gut flora of mice by 16 S rRNA high-throughput sequencing. Methods Twelve specific pathogen free(SPF) C57 BL/6 J mice were randomly divided into CFA group and mock group, with 6 mice in each group. Chronic inflammatory pain model was established by intraplantar injection of CFA in the right posterior pelma of C57 BL/6 J mice. In the control group, normal saline was injected by intraplantar injection in the same position. Two weeks later, the mice were euthanized, and the feces in the colon were collected. The feces of two mice in the same group were mixed, detected and analyzed by 16 S rRNA high-throughput sequencing technology. Results Compared with mock group, the abundance and diversity of gut flora in CFA group decreased. The abundance ofFirmicutesand TM7 increased at the phylum level, the abundance ofAerococcus,LactobacillusandDesulfovibrioincreased significantly at the family and genus level, while the abundance ofPsychrobacter,Prevotella,OscillospiraandBifidobacteriumdecreased significantly compared to mock group. In addition, many biomarkers were found from the level of the phylum to the genus. Conclusion The gut microflora structure, especially the dominant flora, has changed significantly in mice with chronic inflammatory pain, which can provide basis for the treatment of microecological imbalance caused by chronic inflammatory pain and the improvement of patients′ negative emotions through “gut brain axis”.