The thin film deposited by electron beam physical vapor deposition (EB-PVD) on rotating substrate was approached via a kinetic Monte Carlo (KMC) algorithm on a “surface” of tight-packed rows. The motivation is to study the surface morphology distribution of thin film along the substrate radial. Effective deposition rate model and effective incident angle model were established along the substrate radial. Two phenomena are incorporated in the KMC simulation: adatom-surface collision and adatom diffusion. The KMC simulations show that the surface roughness of thin film is small and the changing of surface roughness is small near the side of rotation axis, however, the surface roughness is big near the side of substrate edge, and the surface roughness increases quickly with the increasing of substrate radius when r>300 mm. The simulation results indicate that the effective incident angle is the main factor to cause the changing of surface roughness: the effective incident angle does not reach critical value and the deposition rate difference is small when the radius is less than 300 mm, so the surface roughness of thin film in the scope is small and its changing is small, but when r>300 mm, the effective incident angles increase sharply with radius increasing and all of them are above the critical value, which cause surface roughness of thin film to increase quickly. Experiments reveal that the KMC method can predict surface roughness distribution of thin film deposited by EB-PVD on rotating substrate.