Cement paste is a material with heterogeneous composite structure consisting of hydrated and unhydrated phases at all length scales that varies depending upon the degree of hydration. In this paper, a method to model cement paste as a multiphase system at molecular level for predicting constitutive properties and for understanding the constitutive mechanical behavior characteristics using molecular dynamics is presented. The proposed method creates a framework for molecular level models suitable for predicting constitutive properties of heterogeneous cement paste that could provide potential for comparisons with low length scale experimental characterization techniques. The molecular modeling method followed two approaches: one involving admixed molecular phases and the second involving clusters of the individual phases. In particular, in the present study, cement paste is represented as two-phase composite systems consisting of the calcium silicate hydrate (CSH) phase combined with unhydrated phases tricalcium silicate (C3S) or dicalcium silicate (C2S). Predicted elastic stiffness constants based on molecular model representations employed for the two phases showed that, although the individual phases have anisotropic characteristics, the composite system behaves as an isotropic material. The isotropic characteristics seen from two-phase molecular models mimic the isotropic material nature of heterogeneous cement paste at engineering scale. Further, predicted bulk modulus of the composite system based on molecular modeling is found to be high compared to the elastic modulus, which concurs with the high compression strength of cement paste seen at engineering length scales.