Reconstruction of subarticular bone defects is an intractable challenge in orthopedics. The simultaneous repair of cancellous defects, fractures, and cartilage damage is an ideal surgical outcome. 3D printed porous anatomical WE43 (magnesium with 4 wt% yttrium and 3 wt% rare earths) scaffolds have many advantages for repairing such bone defects, including good biocompatibility, appropriate mechanical strength, customizable shape and structure, and biodegradability. In a previous investigation, we successfully enhanced the corrosion resistance of WE43 samples via high temperature oxidation (HTO). In the present study, we explored the feasibility and effectiveness of HTO-treated 3D printed porous anatomical WE43 scaffolds for repairing the cancellous bone defects accompanied by split fractures via in vitro and in vivo experiments. After HTO treatment, a dense oxidation layer mainly composed of Y2O3 and Nd2O3 formed on the surface of scaffolds. In addition, the majority of the grains were equiaxed, with an average grain size of 7.4 μm. Cell and rabbit experiments confirmed the non-cytotoxicity and biocompatibility of the HTO-treated WE43 scaffolds. After the implantation of scaffolds inside bone defects, their porous structures could be maintained for more than 12 weeks without penetration and for more than 6 weeks with penetration. During the postoperative follow-up period for up to 48 weeks, radiographic examinations and histological analysis revealed that abundant bone gradually regenerated along with scaffold degradation, and stable osseointegration formed between new bone and scaffold residues. MRI images further demonstrated no evidence of any obvious damage to the cartilage, ligaments, or menisci, confirming the absence of traumatic osteoarthritis. Moreover, finite element analysis and biomechanical tests further verified that the scaffolds was conducive to a uniform mechanical distribution. In conclusion, applying the HTO-treated 3D printed porous anatomical WE43 scaffolds exhibited favorable repairing effects for subarticular cancellous bone defects, possessing great potential for clinical application.