This study examined anti-cancer compounds present in the chloroform extract of the Chinese medicine formula Shenqi San (CE-SS). Silica gel column chromatography, Sephadex LH-20, octadecylsilyl (ODS) column chromatography, and high performance liquid chromatography (HPLC) were used to separate the compounds from CE-SS. The structural formulas of the separated compounds were determined using 1D H-1 and C-13 experiments as well as high resolution electrospray ionization mass spectroscopy (HRESIMS). The corresponding results were compared with the reported literature data. A total of six compounds were separated and their structures were identified on the basis of corresponding spectroscopic and physico-chemical properties. They were Saikogenin F (I), Prosaikogenin D (II), Prosaikogenin F (III), beta-sitosterol (IV), 3 beta,16 beta,23-trihydroxy-13,28-epoxyurs-11-ene-3-O-beta-D-glucopyranoside (V), and methyl ursolic acid (VI). The separated compounds were evaluated in vitro for their inhibitory ability against the proliferation of A549 cells via MTT assay. Apoptosis was investigated using Annexin V-FITC/propidium iodide (PI) by flow cytometry. Apoptosis-associated proteins were examined by Western blotting. All the compounds were observed to have inhibitory activities against the proliferation of A549 cells to different degrees. Flow cytometry showed that compound V increased the proportion of apoptotic A549 cells in a dose-dependent manner. Western blotting showed that compound V increased the expression of Bax, cleaved-caspase-3, cleaved-caspase-9 and cleaved-poly ADP-ribose polymerase (PARP), and decreased the expression of Bcl-2. These results indicated that compound V featured a significant inhibitory effect on A549 cells when compared with other compounds, and it may be considered a potential drug against cancers.