Bone tissue engineering is a promising way to repair of bone defects. To choose a proper scaffold is still a disputable problem in bone tissue engineering. This study aimed to compare the effects of repairing critical calvarial defects with the compounds of autogenous bone marrow stromal cells (BMSCs) and coral hydroxyapatite(CHA), hydroxyapatite/ tricalcium phosphate (HA/TCP), poly(lactide-co-glycolide) (PLGA) and alginate (AG). The results showed that CHA and AG were satisfactory bone tissues engineering scaffolds among the four kinds of materials. BMSCs/CHA and BMSCs/AG are promising techniques for reconstruction of bone defects.