Traditional Chinese medicine therapy, which can serve as adjuvant therapy for cancer treatment, has no obvious side effects on the human body. Geniposide (GEN), one of the main iridoid glycosides in gardenia fruit, has been widely reported to have anti-cancer effects. In this study, we aimed to inspect whether GEN could inhibit proliferation and promote the apoptosis of human breast cancer cells (MCF-7). In order to better predict the efficacy of GEN, we have prepared the Cs/Gel composite scaffolds by 3D printing technology to mimic the MCF-7 cell growth microenvironment. The prepared Cs/Gel scaffold has good mechanical properties and biocompatibility, which can provide a more accurate platform for drug screening. The semi-inhibitory concentration (IC50) evaluated by CCK-8 assay was 16.06 mg/mL (24 h), 14.85 mg/mL (48 h), and 13.14 mg/mL (72 h). After exposed to GEN for 48 h, the cancer cell survival rate reduced from 69.15 +/- 2.86% (13 mg/mL) to 20.97 +/- 3.24% (16 mg/mL). Although the inhibitory effect was weaker in the 3D culture system, it also managed to inhibit cell proliferation and induce cell apoptosis. Besides, Live/Dead staining, Hematoxylin-Eosin (H&E) staining and SEM evaluation were also conducted to estimate the anti-cancer effect of GEN in 2D and 3D cultures. The results indicate that GEN has an anti-cancer effect based on a timeand dose-dependent manner.