Aiming at the problem of scaffold degradation in bone tissue engineering, we studied the feasibility that controlls bone defect repair effect with the inhomogeneous structure of scaffold. The prediction model of bone defect repair which contains governing equations for bone formation and scaffold degradation was constructed on the basis of analyzing the process and main influence factors of bone repair in bone tissue engineering. The process of bone defect repair and bone structure after repairing can be predicted by combining the model with finite element method (FEM). Bone defect repair effects with homogenous and inhomogeneous scaffold were simulated respectively by using the above method. The simulation results illustrated that repair effect could be impacted by scaffold structure obviously and it can also be controlled via the inhomogeneous structure of scaffold with some feasibility.