Due to the obvious multi-scale effect of the through silicon via (TSV) and the microbump structure, a large number of meshes need to be generated during mechanical simulation modeling of 3D packaging microsystem. Resonable equivalent processing could reduce the mesh number and improve simulation efficiency. However, the actual microstructure shape may be lost, resulting in larger simulation errors when the conventional equivalent method of square column was applied. Thus, determination methods of the homogenization model parameters were proposed for actual microstructure shapes. Based on the elastic mechanics theory, the equivalent calculation methods of various material parameters of cylindrical structures such as TSV interposer layer were derived in this paper. Further, by using the derived results and based on the delamination idea, the equivalent calculation method of material parameters after homogenization of microbump/underfill layer with drum ball morphology was given. Compared with the existing methods, the proposed method considered the true morphological characteristics of microsystem structures, so the calculation efficiency was higher, and the consistency of the results was better.