In this paper, we treated the Ni$_3$Al based alloy samples with intense pulsed ion beams (IPIB) at the beam parameters of 250KV acceleration voltage, 100 - 200 A/cm$^2$ current density and 60 u pulse duration. We simulated the thermal-mechanical process near the surface of Ni$_3$Al based alloy with our STEIPIB codes. The surface morphology and the cross-section microstructures of samples were observed with SEM, the composition of the sample surface layer was determined by X-ray Energy Dispersive Spectrometry (XEDS) and the microstructure on the surface was observed by Transmission Electron Microscope (TEM). The results show that heating rate increases with the current density of IPIB and cooling rate reached highest value less than 150 A/cm$^2$. The irradiation of IPIB induced the segregation of Mo and adequate beam parameter can improve anti-oxidation properly of IC6 alloy. Some craters come from extraneous debris and liquid droplets, and some maybe due to the melting of the intersection region of interphase. Increasing the pulse number enlarges average size of craters and decreases number density of craters