Background: Postoperative ileus (POI) is a temporary disturbance in gastrointestinal motility following surgery, and intestinal inflammatory response plays a critical role in the pathogenesis of POI. Wuda granule (WDG), a gastrointestinal prokinetic Chinese herbal medicine, is prescribed to promote recovery of gastrointestinal function after abdominal surgery. However, it has remained unclear whether WDG shows anti-inflammatory effects in POI. In the present study, we investigated the effects of WDG in a rat POI model and attempted to clarify the detailed mechanisms of action. Method: Experimental POI was induced in adult male SD rats by intestinal manipulation (IM). WDG were orally administered after surgery at the same points (6 h, 12 h, 18 h, 24 h). Histological changes of mesenterium, levels of cytokines, and CD68 and iNOS expression were determined in rats treated or not with WDG. We also investigated the transcriptome profile of rats treated with WDG in a POI model. Results: Experimental POI in rats was characterized by a marked intestinal and systemic inflammatory response. WDG significantly inhibited the infiltration of neutrophils and macrophages, reduced the levels of IL-6, and CRP, and inhibited protein expressions of CD68 and iNOS in mesentery. Comparison analysis showed that there are 1432 differentially expressed genes (DEGs) between the POI and CON sample, whereas 331 DEGs between the WDG -treated sample and the PO/ group. And 16 DEGs were shared by the POI vs CON and WDG vs POI groups, among which 6 hub genes associated with immune system processes were identified and verified. Conclusions: WDG treatment ameliorates the impaired gastrointestinal motility in the rat model of POI through inhibiting the inflammatory response of mesentery.