To elucidate the toughening mechanism in rubber particle modified semi-crystalline polymers in which the average matrix ligament thickness plays important roles, the micro-to mesoscopic deformation behavior of rubber/semi-crystalline polymer blends was modeled by using large-deformation finite element homogenization method. In this paper, the deformation behavior of three kinds of models which have different size of rubber particles was investigated. A series of computational simulation clarified that highly localized deformation is induced by the initial orientation of lamellae at interface region for the case of smaller size of rubber particles, and it produces larger strain in the matrix due to localization and propagation of the deformation zone. Furthemore, the microscopic deformation is mainly absorbed by not only a slip along chain direction in the crystalline phase, but also interlamellar shear in the amorphous phase, which must be closely related to the toughening mechanism of the rubber/semi-crystalline polymer blends.