Microcapsules are used in a wide range of applications, especially in self-healing composite materials and phase change materials. There is a growing body of literature that recognizes the importance of reinforcement on the mechanical properties of composites, however the effect of microcapsules during service needs to be further investigated. In this study, numerical investigations were conducted to examine the effects of the various geometric parameters on the mechanical behavior of microcapsules-based composites. The effective Young’s modulus and Poisson’s ratio of core-shell microcapsules distributed in a continuous matrix were predicted. A detailed three-dimensional finite element modeling (FEM) was presented. The numerical results were compared with a hierarchical proposed analytical model for three-constituent composites. Good agreements were achieved.