This paper presents a gas-kinetic scheme to solve the multiple temperature kinetic model (MTKM), which was proposed in J. Comput. Math. 29(6) (2011) 639–660, for the study of non-equilibrium flows. The MTKM is a two-stage particle collision model possessing an intermediate quasi-equilibrium state with a symmetric second-order temperature tensor. A gas-kinetic finite volume scheme is developed for the numerical solution of the MTKM in the continuum and transition flow regimes. The gas-kinetic scheme is designed for the updating of macroscopic variables, which include the conservative flow variables and the multiple temperature field. In order to validate the kinetic model, the gas-kinetic scheme is used in the study of lid-driven cavity flows in both continuum and transition flow regimes. The numerical results predicted by the MTKM are compared with those from the direct simulation Monte Carlo (DSMC) method, the Navier–Stokes equations (NSE), and the early three-temperature kinetic model (TTKM) proposed in Phys. Fluids 19, 016101(2007). It is demonstrated that the MTKM has obvious advantages in comparison with the NSE and the TTKM in capturing the non-equilibrium flow behavior in the transition flow regime. One distinguishable phenomenon captured by the MTKM is that in the transition flow regime the heat flux direction can be from a low temperature to a high temperature region, which violates the Fourier’s law of continuum flows. The MTKM provides a more accurate physical model than the NSE for the non-equilibrium flows.