Defatting is an important procedure for the preparation of bone grafts because lipids in bone grafts strongly influence the osteointegration. Lipases have been widely used in different fields. However, study on the application to defatting process for bone grafts preparation has never been found so far. In this study, bone samples were treated respectively by lipase, NaHCO3/Na2CO3, acetone and deionized water. The lipids content of processed bone grafts was calculated in Soxhlet extractor method. Surface morphology of the bone grafts was observed under scanning electron microscope (SEM). DNA content of processed bone grafts was measured. Cytocompatibility was evaluated by co-culturing mouse preosteoblasts (MC3T3-E1) on defatted bone cubes. Proliferation rates of MC3T3-E1 were examined by cell counting kit-8 (CCK-8) assay. No statistically significant difference was found between lipids amount of bone processed by lipase (0.46 ± 0.16 %) and acetone (1.11 ± 0.13 %) (P > 0.05). Both of them were significantly lower than that in groups processed by Na2CO3/NaHCO3 (3.46 ± 0.69 %) and deionized water (8.88 ± 0.18 %) (P = 0.000). Only cell debris were discovered over the surface of bone processed by lipase or acetone, while lipid droplets were observed on bone processed by Na2CO3/NaHCO3 or water by SEM. The difference of DNA concentration between the bone processed by lipase (3.16 ± 0.81 ng/μl) and acetone (4.14 ± 0.40 ng/μl) is not statistically significant (P > 0.05). Both of them are significantly lower than that groups processed by Na2CO3/NaHCO3 (5.22 ± 0.38 ng/μl) and water (7.88 ± 0.55 ng/μl) (P < 0.05). MC3T3-E1 cells maintained their characteristic spreading on the trabecular surfaces of bone processed by lipase. There were no statistically significant differences among absorbance of lipase, acetone groups in CCK-8 assay. The application of lipase to bone tissue defatting appears to be a very promising technique for bone grafts preparation.