Based on the CT data of a patient’s femur, a three-dimensional FEA medical model of femur treated with AHJC was rebuilt, under the load conditions of 1.5 and 2.5 times standard body weight (70 kg), and the biomechanics of the model were analyzed for three different healing periods by FEA. The results showed that in the initial period post-operation, the Young’s modulus of tissue in host-donor junction area was low, and there were serious stress concentrations in the middle of junction area and the bone cement, meanwhile, the maximum stress in bone cement was higher than the compress strength of it, so it would be in the risk of crash. With the growth of new bone in host-donor junction area, the Young’ modulus of the tissue increased, and the stresses shielding and concentration in the junction area and bone cement decreased greatly. The stress distribution in host-donor junction area will be in the level of normal bone, after the wound healed and the tissue in host-donor junction area gradually grew to be mature bone. Porous hydroxyapatite (HA) ceramics used as bone-scaffold in the host-donor junction area would decrease the stress shield and concentration in the junction area, and improve the biomechanical safety properties for clinic application of the AHJC.