The hydrodynamic effects of molten surface of titanium alloy on the morphology evolution by intense pulsed ion beam (IPIB) irradiation are studied. It is experimentally revealed that under irradiation of IPIB pulses, the surface morphology of titanium alloy in a spatial scale of μm exhibits an obvious smoothening trend. The mechanism of this phenomenon is explained by the mass transfer caused by the surface tension of molten metal. Hydrodynamic simulation with a combination of the finite element method and the level set method reveals that the change in curvature on the molten surface leads to uneven distribution of surface tension. Mass transfer is caused by the relief of surface tension, and meanwhile a flattening trend in the surface morphology evolution is achieved.