Background and aim Traditional Chinese medicine has received attention as a potential method for treating STC. This investigation aimed to identify the target for therapy and the mechanism of Tongyou Decoction in STC by employing a rat model induced with a compound diphenoxylate suspension. Methods Body weight, stool frequency, fecal water content, and intestinal transit were recorded, while colonic histology, gastrointestinal hormones, inflammatory cytokines, and ICC/ANO1/PDGFRα-SK3 pathway components were assessed using standard histological and molecular techniques. Results Tongyou Decoction dose-dependently improved intestinal transit and stool parameters, attenuated colonic inflammation, normalized hormone profiles, and reversed dysregulated expression of PDGFRα, C-kit, SK3, and ANO1. Conclusion Tongyou Decoction improved intestinal transit, reduced colonic inflammation, and favorably modulated gastrointestinal hormones and ICC/ANO1/PDGFRα-SK3 pathway components in diphenoxylate-induced STC rats. These findings suggest that Tongyou Decoction may have potential as an adjunct therapy for slow transit constipation, but further studies are required to confirm its efficacy and safety in humans.