The phytochemical profiles, antioxidant activity and antiproliferative mechanism of two goji berry varieties were investigated in the present study. In contrast to Lycium barbarum L. (LB), Lycium ruthenicum Murr. (LRM) showed stronger antioxidant activity evaluated by ORAC, PSC and CAA assays, which might be attributed to its higher total phenolics and total flavonoids. However, LB contains greater contents of VE and carotenoids compared to LRM, which may endow LB with other unique functions instead of antioxidant activity. Additionally, high dose LRM showed a stronger capability in terms of cell cycle arrest and cell apoptosis induction of MDA cells with increments of 17.85% cells blocked at the G1 phase and 50.49% cells achieving early apoptosis compared with the control group. Although supplementation with LB increased the number of cells in the G1 phase by 10%, its effect on inducing cell apoptosis was not ideal. Furthermore, both LRM and LB activated the proliferation-related p53 signaling pathway including p53, p21, CDK4, Cyclin E, Bax and Caspase3, but LB failed to downregulate bcl-2 and CDK2 levels, indicating the weaker antiproliferative effect of LB. The present findings indicated LRM and LB as potential candidates for managing the proliferation of cancer cells and improving human health.