The objective of this work is to develop a multiscale modeling tool of copolymers with long chains. We propose an enhanced coarse-graining method of thermoplastic polyurethane (TPU) with three beads. The proposed coarse-graining provides an accurate molecular modeling tool to keep the molecular interaction together with computational efficiency. The coarse-grained model with three beads is further improved with pressure-correction of the force-field. The improved coarse-grained model holds similar properties of a bulk model of TPU—varying density with temperature, a close density value of TPU at 1 atm, and the phase separation. Equating potential energy densities of the coarse-grained model to the strain energy functions of the continuum model at volumetric and isochoric deformation modes, bulk and shear moduli of TPU are directly obtained and used to estimate Young's modulus and Poisson's ratio. The molecular simulation with the coarse-grained model of TPU demonstrates its much greater bulk modulus than the shear modulus, which is typically observed in elastomers. Modifying the coarse-grained model of TPU with hard and soft segments, we successfully demonstrated the material design of bulk modulus and Poisson's ratio by varying hard and soft segments at the molecular level. The proposed coarse-graining tool will pave a new way to explore the multiscale modeling of copolymers with long chains and can be directly applied to the multiscale modeling of other thermoplastic elastomers (TPE).