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In this paper, a unified gas-kinetic scheme (UGKS) with simplified multi-scale numerical flux is proposed for the thermodynamic non-equilibrium flow simulation involving the excitation of molecular vibrational degrees of freedom in all flow regimes. The present UGKS keep the basic conservation laws of the macroscopic flow variables and the microscopic gas distribution function in a discretized space. In order to improve the efficiency of the UGKS, a simplify multi-scale numerical flux is directly constructed from the characteristic difference solution of the kinetic model equation. In addition, a new BGK-type kinetic model for diatomic gases is proposed to describe the high-temperature thermodynamic non-equilibrium effect, which is a phenomenological relaxation model with the continuous distribution modes of rotational and vibrational energies. In present model, the equilibrium distribution functions is constructed by using a multi-dimensional Hermitian expansion around the Maxwellian distribution to achieve the correct Prandtl number and proper relaxation rate of heat fluxes. Furthermore, the application of the unstructured discrete velocity space (DVS) and a simple integration error correction reduce the number of velocity mesh significantly and make the present method be a efficient tool for simulations of flows in all flow regimes. The new scheme are examined in a series of cases, such as Sod's shock tube, high non-equilibrium shock structure, hypersonic flow around a circular cylinder with Knudsen (Kn) number Kn = 0.01, and the rarefied hypersonic flow over a flat plate with a sharp leading edge. The present UGKS results agree well with the benchmark data of DSMC and the other validated methods.