In Hard Disk Drives, lubricants are very important materials to reduce head and disk wear. Therefore, it is necessary to know the lubricant depletion under flying heads. Lubricant depletion due to flying heads has been studied experimentally. We developed simulation program to calculate numerically the change in lubricant thickness under a flying head on a thin-film magnetic disk from 10nm thick lubricant film. In recent HDDs, the lubricants thickness has become molecularly thin and polar lubricants have been used. In this paper, we took account of thickness-dependent lubricants diffusion and viscosity in our simulations to calculate a 1.2 nm thick polar lubricant film used in recent HDDs. The simulated results considering the thickness-dependent diffusion and viscosity showed that depletion was small in molecularly thin lubricant films. We considered it necessary to include thickness-dependent diffusion and viscosity in lubricant depletion simulation.