In this letter, the influence on the beam quality due to cumulative effect of the inner channel thermal deformation in the high energy laser system with unstable resonator is researched. Firstly, three typical laser powers of 50, 100, and 150 kW are selected to analyze thermal deformation of mirror by the finite element analyze of thermodynamics instantaneous method. Then the wave front aberration can be calculated by ray-tracing theory. Finally, Strehl ratio and Zernike aberration coefficients of the vacuum far-filed beam can be calculated and comparably analyzed by Fresnel diffraction integration. The theory and simulation results show that due to the effect of inner channel thermal deformation, eccentric phenomenon and astigmatism of far-filed beam emerge, and peak power and the focused ability decrease. With the increasing of reflective times, Strehl ratio decrease, and tilt, astigmatism and coma of x direction gradually increase, which become the main aberration. The results can provide the reference to the thermal aberration analysis for high energy laser system and can be applied to the field of laser nuclear fusion and laser weapon, etc.