In recent years, high entropy alloys (HEAs) have attracted significant attention due to their excellent physical, chemical, mechanical properties, and good irradiation resistance, thus are considered as potential candidates for fission and fusion structural applications. CoCrFeMnNi HEA was irradiated by high intensity pulsed ion beam (HIPIB) to investigate the effects of thermal shock irradiation on its microstructure, surface morphology and mechanical properties. It was found that CoCrFeMnNi HEA maintained the face-centered cubic single-phase structure after HIPIB irradiation. The ion beam effect of irradiation produced numerous defects such as vacancies and stacking faults within the range of carbon ions. While the thermal effect reduced vacancy concentration beyond the ion range by promoting the recombination of vacancies with interstitials, and decreased the nano-hardness of CoCrFeMnNi HEA. The thermal effect and shock wave effect promoted the migration of vacancies and formed defects such as stacking faults etc. far beyond the ion range in CoCrFeMnNi HEA. Because of the very compositional complexity, the high-level chemical disorder and local lattice distortion of CoCrFeMnNi HEA, the lattice parameter was almost unchanged after HIPIB irradiation. Even if the temperature reached the melting point of CoCrFeMnNi HEA, there was no crack on the surface after surface remelting and rapid cooling. CoCrFeMnNi HEA showed good thermal stability and thermal shock irradiation resistance..