Reaction-induced phase separation occurs during the curing reaction when a thermoplastic resin is dissolved in a thermoset resin, which enables toughening of the thermoset resin. As resin properties vary significantly depending on the morphology of the phase-separated structure, controlling the morphology formation is of critical importance. Reaction-induced phase separation is a phenomenon that ranges from the chemical reaction scale to the mesoscale dynamics of polymer molecules. In this study, we performed curing simulations using dissipative particle dynamics (DPD) coupled with a reaction model to reproduce reaction-induced phase separation. The curing reaction properties of the thermoset resin were determined by ab initio quantum chemical calculations, and the DPD parameters were determined by all-atom molecular dynamics simulations. This enabled mesoscopic simulations, including reactions that reflect the intrinsic material properties. The effects of the thermoplastic resin concentration, molecular weight, and curing conditions on the phase-separation morphology were evaluated, and the cure shrinkage and stiffness of each cured resin were confirmed to be consistent with the experimental trends. Furthermore, the local strain field under tensile deformation was visualized, and the inhomogeneous strain field caused by the phase-separated structures of two resins with different stiffnesses was revealed. These results can aid in understanding the toughening properties of thermoplastic additives at the molecular level.