Rheology and tribology become more and more critical issues in order to satisfy the harsh requirements for ultra‐small head/media spacing HDDs. In this communication, MD simulations with a bead/spring model were employed to examine the nano‐rheological response of nonfunctional and functional PFPEs by analyzing the shear viscosity of nanoscale PFPE films and the relaxation processes as a function of wall interaction/separation and endgroup functionality. Our simulation results indicate that thin PFPE films show more solid‐like behavior, especially under high shear rate. The film deformation and shear viscosity change by tuning the film thickness and the endgroup functionality was discussed in conjunction with the relaxation processes.