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The treatment of large-area bone defects is a huge challenge and the current research hot spot is to prepare composite materials to promote the new bone formation. In this study, the rat skull defect was repaired by implanting pure wollastonite and hydroxyapatite composites, which proved that it has a good effect on the treatment of bone defects. 60 SD rats were used as research objects. The animals were randomly divided into wollastonite group, wollastonite-hydroxyapatite composite group and hydroxyapatite group. The three groups of bone scaffolds were filled into the rats’ skull defects. At 6 and 12 weeks after surgery, we conducted Micro-CT analysis, HE staining, Masson trichrome staining, Alizarin red staining and Microfil analysis, to assess the therapeutic and regeneration effects of three groups. At 6 weeks after implantation, the morphology results showed that little newly formed bone was observed in wollastonite group, on the contrary, more new bone in the surgical defects formed in the wollastonite-hydroxyapatite composite group and hydroxyapatite group. At 12 weeks after surgery, histology analyses revealed that the regenerated bone became more mature in each groups. The morphology showed that the maturity of new bone was improved and the scaffold material was partially absorbed in wollastonite-hydroxyapatite composite group. CT scan observation showed that on the coronal plane, the defect repair area of wollastonite-hydroxyapatite composite group was integrated with the surrounding normal bone tissue, and the sacffold material was tightly integrated with the defect edge. The results of Microfil showed that compared with wollastonite group and hydroxyapatite group, wollastonite-hydroxyapatite composite group formed more blood vessels after 12 weeks of surgery. The wollastonite-hydroxyapatite composite biomaterial can promote the formation and growth of new bone in the defect area, and it is considered safe.