In this work, the rarefied Couette flow of diatomic gases with thermal nonequilibrium effects is investigated by the direct simulation Monte Carlo (DSMC) method, and a macroscopic computational model is developed to consider the local rarefaction effects for diatomic gases in the near-continuum regime. The nonlinear transport properties of the diatomic gases are studied, indicating that effective viscosity and effective translational thermal conductivity in the shear nonequilibrium state are affected by translational nonequilibrium effects, which obey the same laws for both monatomic and diatomic gases. The transport coefficients of internal energy modes are affected by both translational nonequilibrium and internal energy relaxation, therefore, the effective rotational and vibrational thermal conductivities are related to the effective viscosity through a modified Eucken relation that accounts for internal energy relaxation. Conclusively, effective constitutive relations are newly established as a function of the shear nonequilibrium parameter and the modified Eucken factors for thermal nonequilibrium flows, and these are integrated into the macroscopic two-temperature model. Subsequently, it is assessed in the simulation of hypersonic flows over flat plates and cylinders at various Knudsen numbers. The results show that the surface shear stress and heat flux obtained by the proposed model agree well with the DSMC results, indicating significantly improved performance compared to the conventional Navier–Stokes two-temperature model for hypersonic flows in the near-continuum regime.