Composite materials with periodic microstructures are commonly used in engineering. Numerical homogenization with finite element method (FEM) has proven fairly effective to determine the mechanical properties of a range of composite materials. However, traditional FEM fails to evaluate the effective mechanical properties for incompressible constituents due to volumetric locking problem in numerical analysis. In this paper, a novel selective smoothed finite element method (S-FEM) in multi-material domain using triangular and tetrahedral elements is proposed to overcome the locking problem in the numerical homogenization of incompressible materials. The implementation of S-FEM is easy without additional parameters. A number of characterization examples for porous, multiphase, tissue scaffold composites are presented to demonstrate the effectiveness of the proposed SFEM homogenization in handling incompressible base materials.