Allograft reconstruction is an acceptable procedure for the recovery of normal anatomy after the bone tumor resection. During the past few years, several automated methods have been proposed to select the best anatomically matching allograft from the virtual donor bone bank. The surface-based automated method uses the contralateral healthy bone to obtain the normal surface shape of the diseased bone, which could achieve good matching of the defect and the selected allograft. However, the surface-based method focuses on the matching of the whole bone so that the matching of the contact surface between the allograft and the recipient bone may not be optimal. To deal with the above problem, we propose a cutting contour based method for the allograft selection. Cutting contour from the recipient bone could reflect the structural information of the defect and is seldom influenced by tumor. Thus the cutting contour can be used as the matching template to find the optimal alignment of the recipient bone and the allograft. The proposed method is validated using the data of distal femurs where bone transplantation is commonly performed. Experimental results show that the proposed method generally outperforms the surface-based method within modest extra time. Overall, our contour-based method is an effective complementary technique for allograft selection in the virtual bone bank.