Objective To analyze and compare the application of different modeling methods used in the construction of bio-tissue 3D finite element model. Methods: Based on the same serial CT images, to construct calcaneus 3D finite element model with the implementing of three different methods (direct, indirect, and composite methods), then to carry out simple loading calculation on two models under the same condition. Results The number of nodes and elements generated from direct modeling are 31386 and 115646, while that from indirect modeling are 22832 and 15403, respectively; and that of composite method are 13050 and 46654, respectively. The results reveal the similar distributing of von Mises Stress of three models, with some local differences, but the special stress values show greater difference. Conclusion The exterior roughness of model and the form of material assignment have great effect on the calculating result of models. Different modeling method has their own appropriate application fields. For the purpose of medical research, it would be better to combine the two methods to promote the development of computational biomechanics.