In this paper, a kinetic Boltzmann model equation with internal degrees of freedom is established for thermodynamic non-equilibrium multi-component polyatomic gas mixture by using continuous energy levels to deal with rotational energy and vibrational energy. The normalization and conservativeness of the kinetic model are analyzed and proved. Then, numerical algorithm and wall boundary conditions for solving the model equation are given. Then, normal shock-wave structure flow problem and pressure/temperature gradient driven micro-channel flow problem for the two-component gas mixture are used to verify the reliability of the model. The simulation results are in good agreement with those obtained by other methods, which verifies the reliability of the model and algorithm in this paper. Finally, taking 25 N attitude control engine two-dimensional profile as the object, the study for two-dimensional profile nozzle internal and external mixed flow problem is carried out, and the influence of different inlet rarefaction levels on the molecular transports of mixed flow field and the molecular transport phenomena of mixed flow field with different number of components are discussed.