3D printing technology has various advantages, and the incorporation of bioactive substances into the 3D printed scaffold provides the biological and architectural characteristics of the scaffolds, which is very important for obtaining a good osseointegration effect. In this relation, this study prepared a novel porous hollow cage poly(lactic acid) (PLA) 3D printed scaffold and combined recombinant human bone morphogenetic protein-2 (rhBMP-2) and/or mesenchymal stem cells (MSCs) with Biogel composed of gelatin and alginate. Then, the scaffolds were used to evaluate the resulting bone regeneration through both in vitro and in vivo tests. The experimental group was divided into four groups as follows: only PLA scaffold (PLA); PLA scaffold filled with BMP-2 loaded on Biogel (P-BG-B2); PLA scaffold filled with MSCs encapsulated Biogel (P-BG-M); PLA scaffold filled with both BMP-2 and MSCs loaded on Biogel (P-BG-B2-M). Then in vitro results showed that the PLA-Biogel-based scaffold increased cell proliferation, and the P-BG-B2-M group showed a higher alkaline phosphatase activity and bone-related gene expression than was seen with the P-BG-M group at all the time points. It was shown that four weeks post-operative micro-CT analysis showed that within the defect site the P-BG-B2 group had a significantly higher percent bone volume (BV/TV) than the PLA group and P-BG-M group. And, out of the defect site, the P-BG-B2-M group BV/TV was shown significantly higher than the PLA group (p < 0.05). Histologically, defects in the P-BG-B2-M group showed a homogeneous new bone distribution, however the P-BG-B2 group and P-BG-M group presented a notably higher bone formation in the internal region than in the proximal region of the bone defect site. In conclusion, the 3D PLA-Biogel-based scaffold adapted rhBMP-2 and MSCs with carrier PLA showed good biocompatibility and high possibility as an effective and satisfactory bone graft material.