Abstract Objective The aim of the study was to investigate the effects of Chinese herbal formula Weichang'an (WCA) on the proliferation and mitochondria-mediated apoptosis of human gastric cancer cells. Methods Cell Counting Kit-8 (CCK8) was used to evaluate the antiproliferative activity of WCA on MKN45 cells; Giemsa staining was used to investigate cell colony formation; flow cytometry was used to analyze cell cycle, apoptosis rate, and caspases activation; and Hoechst staining was used to analyze the morphology of cell nuclei. The mitochondrial membrane potential was analyzed by both flow cytometric measurements and fluorescence microscopy. Western blot was used to analyze the protein levels of pro-caspase-3, Bcl-2, Bax, and Bcl-X. MKN45 cells were subcutaneously injected into the right forelimb of 16 nude mice to establish the tumor xenograft model, and a total of 12 nude mouse tumor xenograft models were successfully created. The nude mice were divided into the control group and the WCA-treated group. The two groups received normal saline and WCA treatment at 35.49 g/kg by a single daily oral gavage for 21 days. The body weight and tumor size of the nude mice were measured twice a week. The ultrastructural changes of subcutaneous tumors were observed by a transmission electron microscope. Results WCA can suppress cell proliferation and colony formation. It can also induce changes in the mitochondrial membrane potential and increase the activities of caspases-3, caspases-8, and caspases-9 in MKN45 cells. WCA induced S-phase arrest and apoptosis in MKN45 cells, and decreased the expression levels of antiapoptotic proteins Bcl-2 and Bcl-X in MKN45 cells, while increasing the expression levels of the proapoptotic proteins Bax and pro-caspase-3 compared with the control group. WCA inhibited the growth of a xenografted MKN45 tumor in nude mice, and the protein levels of Bax and pro-caspase-3 were significantly increased, while Bcl-X and Bcl-2 were reduced compared with the control group. The differences are statistically significant (p < 0.05). Conclusion WCA could suppress the proliferation of gastric cancer cells via mitochondrial apoptosis.