A novel method was developed for calcium deficient hydroxyapatite (CDHA) scaffold 3D printing, through which a bilayer scaffold was fabricated by integral molding of individual CDHA and PLGA. The hydration reaction of α-TCP was utilized to form CDHA, and a mixed solution of gelatin, glycerine, glutaraldehyde was applied as the dispersant and adhesive. The concentration of the glutaraldehyde (1 ‱(v/v)) and the mixing ratio of α-TCP (0.6, 0.8, 1.0, 1.2(g/mL)) was studied in the effect on the forming ability of the CDHA ink. The influence of α-TCP proportion (0.6, 0.8, 1.0, 1.2 (g/mL)) on the formation of CDHA was also researched in phase analysis, morphology and compressive strength measurements. The CDHA/PLGA bilayer scaffold was fabricated with a good combination of the two components by 3D printing. The in vitro degradation, cytotoxicity, and cell proliferation behavior were studied. Meanwhile the in-vivo performances in terms of surgical safety, biodegradation, and osteogenic capacity were investigated with a cortical bone defect model in a rabbit femur. The results showed that the CDHA/PLGA bilayer scaffold had excellent biocompatibility and no cytotoxicity. The scaffolds were successfully implanted and presented remarkable osteogenic capacity within 6 months through analyses in radiography and histology. In conclusion, the method has a potential clinical application in diverse bone repair practices by varied 3D-printing fabrication.© 2020 IOP Publishing Ltd.