Molecular dynamics; simulations have been performed to study the rheological behavior of confined branched (Krytox type and Fomblin Y type) and linear (Demnum type and Fomblin Z type) perfluoropolyethers. Shear thinning of the viscosity is observed in all cases, and the shear thinning rate is in reasonable agreement with experimental results of Demnum and Krytox types. The viscosity of the branched Krytox type is slightly lower than that of the linear Demnum type when confined, although their bulk viscosity values are the same. Further, higher molecular ordering is observed in the Demnum type than:in the Krytox type. However, no viscosity-difference is observed between branched Fomblin Y and linear Fomblin Z types, which have many ether Linkages. No molecular order difference is observed between them either. Accordingly, the side chain effect is expected to decrease because of the molecular flexibility caused by their many ether linkages. The nonbonded interaction energy between an atom and atoms of other molecules is also investigated as a function of the sliding distance using different slider velocities. It is found that short periodic energy changes decrease and long periodic energy changes increase with increasing slider velocity. This is expected to be one of the causes of the decrease in the energy required for the molecules to pass each other within a certain distance and one of the causes for shear thinning.