This study was to compare the effects of three-dimensional (3D) printed bioactive porous titanium alloy scaffolds (3DP-BPTAS) and rhBMP-2/PLA-loaded sustained-release nanospheres (SRNs) in the treatment of bone defects. In this study, the bioactive porous titanium alloy scaffolds (BPTAS) with different pore sizes were prepared by selective laser melting (SLM) technology. The rhBMP-2/PLA SRNs were prepared by the double emulsion solvent volatilization method. The morphology of the two nanomaterials was observed under a scanning electron microscope (SEM). The encapsulation rate (ER), drug loading (DL), and in vitro release rate of the SRNs were detected by enzyme-linked immunosorbent assay (ELISA); and the effects of different particle sizes of BPTAS and SRNs on the proliferation of BMSCs were measured using the Methyl Thiazolyl Tetrazolium (MTT) method. 42 healthy male rabbits were selected and rolled into a control group (no treatment), a model group (the femoral condyle defect model), an A800 group (model + 800 μm of BPTAS), and an A1000 group (model + 1000 μm of BPTAS), an A1200 group (model + 1200 μm of BPTAS), an A1500 group (model + 1500 μm of BPTAS), and an SNR group (model + rhBMP-2/PLA SRNs). There were 6 rabbits in each group, and they were sacrificed 4, 8, and 12 weeks after the surgery. They were performed with general observation, X-ray photography, and histological and biomechanical examinations. According to the Lane-Sandhu bone defect repair tissue X-ray and histological scoring standard, the effect of bone defect repair was evaluated. It was found that the actual pore structure of the scaffold prepared by the SLM process was consistent with the theoretical design. The observation under TEM showed that rhBMP-2/PLA SRNs were approximately round, with an average particle size of 835 nm, and its encapsulation efficiency and drug loading rate were 89.02 ± 5.14% and 0.033 ± 0.004%, respectively. The rhBMP-2/PLA SRNs and BPTAS had no statistically obvious increase in the number of cells after cell treatment compared with the control group (P> 0.05). At 12 weeks postoperatively, the stent bone tissue growing distance (SBTGD) in the SRN group was longer than that in the A1000 group (P< 0.01), and that in the A1000 group was better in contrast to the A800, A1200, and A1500 groups (P< 0.01). The Lane-Sandhu X-ray score of the SRN group was better than other groups (P< 0.05). It suggested that 3DP-BPTAS and rhBMP-2/PLA SRNs could repair the bone defects, and rhBMP-2/PLA SRNs were more conducive to the formation of new bone tissue.