Intense pulsed ion beam (IPIB), featured with pulsed high-power density, has been widely used in the modification of materials. The influence of IPIB irradiation on surface microstructure and phase structure of (TiZrNbTaCr)C ceramics was investigated in this work. Experiments were carried out using TEMP-4M accelerator with peak accelerating voltage, current density, and pulse duration (FWHM) of 220 kV, 150 A/cm2, and 80 ns respectively. Atomic force microscope (AFM), scanning electron microscope and Energy-dispersive X-ray spectroscopy (SEM-EDS), as well as X-ray diffraction (XRD) were used to analyze the surface microstructure and phase structure of (TiZrNbTaCr)C ceramics under IPIB irradiation. The AFM and SEM images showed that the grain size of (TiZrNbTaCr)C increased, and the size and quantity of holes decreased after IPIB irradiation which might improve the erosion resistance of material. After IPIB irradiation, the segregation of Cr and Ta elements were observed by EDS measurement. The phase structure stability of samples under IPIB irradiation was confirmed by XRD and the lattice parameters and crystal spacing was discussed as well.