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Objective: To observe morphological changes of enteric nervous system (ENS)-interstitial cells of Cajal (ICC)-smooth muscle cell (SMC) structure injury in deep muscle nerve plexus offunctional dyspepsia (FD) rats, and the repair of Shuwei Decoction (SD) on it, and to explore its effecton FD., Methods: Totally 72 rats were randomly divided into the control group, the model group, the lowdose SD group, the medium dose SD group, and the high dose SD group, the Mosapride group, 12 ineach group. Rats in the low dose SD group, the medium dose SD group, and the high dose SD group were intragastrically fed with SD at 0.767, 1.534, 3.068 g/mL, respectively. Rats in the Mosapride group were intragastrically fed with Mosapride (1.37 mg/kg). FD rat model with Gan depression Pi deficiency syndrome (GDPDS) was established using complex pathogenic factors. Corresponding liquors were respectively administered to rats in corresponding groups from the 3rd day after modeling. Distilled water(10 mL/kg) was administered to rats in the control group and the model group, once per day for 14 successive days. Rats were sacrificed and small intestine tissues collected for observing ENS-ICC-SMC structure injury using immunofluorescence double labeling, laser scanning confocal microscope, and transmission electron microscope at day 15. Repair of SD on it was also observed., Results: ENS-ICC SMC structure was incomplete, with obvious injury in mutual link of ICC, ICC, SMC, and connecting structure. ENS-ICC-SMC structure was more complete in high, medium, and low dose SD groups, with close link of ICC and SMO. Their connecting structures were in good conditions., Conclusion: SD could keep the integrity of ENS-ICC-SMC structure by promoting regeneration and morphology of ICC, thereby, improving gastrointestinal movement disorder and showing therapeutic effect on FD.