Strain rate effects on surface deformation behavior of exfoliated nylon 66 (PA66)/organoclay nanocomposites have been explored by nanoindentation in present study. Sharp indenter (Berkovich) has been used to indent on the surfaces of polymer/clay nanocomposite with different strain rates. Significant strain-rate hardening has been found consistently existing in both neat PA66 and its nanocomposite systems from surface to subsurface (a few micron deep into the bulk). However, strain rate shows almost no effect on the elastic moduli of the neat system and the nanocomposites. The elastic modulus and hardness increase with the indentation depth due to inhomogeneous distributions of the crystalline morphology as well as clay concentration for the case of the nanocomposites along the indentation direction. The mechanical properties observed are correlated with the inhomogeneous microstructures of the studied systems. The plastic index of PA66 and the nanocomposites have been evaluated as a function of strain rate.