Objective The 4D-FastDIA proteomic method was employed to explore the mechanism of LiqiTongfu massage in treating functional dyspepsia (FD), focusing on its effects on protein expression. Methods 30 rats were categorized into CTL group, MOD group, TN group ( n=10 rats per group), using a random number table approach. Rats in CTL group were fed normally. Rats in the MOD and TN groups were treated with tail clips,ice water, and a non-standard diet. After successful modeling, TN group was treated with LiqiTongfu manipulation for 14 days. Overall health and digestive movement were then assessed, pathological changes in the stomach tissues were monitored, and protein expression levels were measured in each group. Results Rats in CTL group exhibited pure white, thick, and lustrous fur, well-formed stools without odor, and were in good spirits with high activity levels. Rats in MOD group rats displayed dull, disheveled, sparse, and lackluster fur, loose stools with an acidic odor, lethargy, reduced activity levels, and decreased gastric emptying and small intestinal propulsion rates (P<0. 01). Rats in TN group exhibited restored dense, glossy fur, well-formed feces without an acidic odor, and improvements in mental state, activity levels, gastric emptying rate, and small intestinal propulsion rate ( P<0. 01). Hematoxylin-eosin staining showed no clear infiltration of inflammatory cells in the gastric mucosa, and no difference in gastric histopathology across the three groups. Proteomic analysis showed changes in 263 proteins in MOD group compared with CTL group, and changes in 237 proteins in TN group compared with MOD group. The protein expression profiles differed between MOD group and CTL group, but massage treatment reversed the differences in 95 proteins, of which 16 were up-regulated and 79 were down-regulated. Conclusions LiqiTongfu massage therapy can effectively improve FD. This may be related to the regulation of structural proteins, smooth muscle and cell motility-associated proteins, protein activity-regulating proteins, metabolism-related proteins, signal transduction and regulation-related proteins,as well as immune and stress-related proteins.