Two cultivated varieties of Gleditsia sinensis Lam, Shuo Spina Gleditsiae (SSG) and Mi Spina Gleditsiae (MSG), are currently used in China as a mixture of the herb Spina Gleditsia. This work evaluates, for the first time, the difference in cytotoxicity, antioxidant activity, and flavonoid contents between SSG and MSG. Quantification of bioactive flavonoids in the samples was performed using high-performance liquid chromatography. Total antioxidant activity and 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid free radical scavenging assays were used, and the growth inhibitory effects on cancer cells were determined using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide assay. Epicatechin, isovitexin, fisetin, fustin, quercetin, and aromadendrin were qualified and quantified; much higher amounts were found in the extract of SSG than that of MSG. In antioxidant assays, SSG extracts presented stronger effects than those of MSG. The half-maximal inhibitory concentration values of SSG were 46.2 and 47.8 μg/mL, compared with 70.5 and 73.0 μg/mL for MSG against EC109 and HepG2 cancer cells, respectively. It thus brings concern about potential quality issues regarding efficacy, safety for healthy food production, and potential medicinal uses.