Objective To compare the mechanical properties of ilium, scapula, and fibula used for reconstruction of metatarsus deficit. Methods Bone defect was simulated at the first to third metatarsus and fourth to fifth metatarsus using a 3-D foot skeletal model. Defects were then reconstructed using ilium, fibula, and scapula, respectively. The displacements and stresses of the reconstructed defects were evaluated using finite element analysis. Results Variations were shown in displacements and stresses among different metatarsus defects, with the largest variation in the deficit of the first to third metatarsus. The use of ilium for metatarsus defect reconstruction revealed the lowest values in the maximum displacement and stress as compared with scapula and fibula. Conclusion Based on mechanical analysis, it was recommended to repair the bony defects involving several metatarsuses and ilium was the most preferred skeleton for reconstruction.