Postoperative ileus (POI) is a common surgical complication, and its incidence remains high. Shenhuang Plaster (SHP) is a famous traditional Chinese medicine with a definite curative effect on postoperative intestinal dysfunction; however, the mechanisms involved in these effects are unclear. Accordingly, in this study, we constructed a POI mouse model and used the intestinal flora as the target to explore the regulatory effect of SHP on gastrointestinal motility. The results illustrated that SHP applied at the Shenque acupoint promoted the recovery of gastrointestinal motility, relieved intestinal villus atrophy and basal damage caused by POI, protected the integrity of intestinal tissue morphology, and alleviated the inflammatory response in the intestinal tissue of POI model mice. In addition, we clarified the role of the intestinal flora in the occurrence and development of POI, further evaluated the changes in the intestinal flora in each group of mice, and analysed the regulatory effect of SHP on the intestinal flora in mice with POI. The results suggested that SHP might improve gastrointestinal motility disorder in POI mice by effectively regulating intestinal flora.