Nanoindentation is widely used to characterize the mechanical and interfacial properties of thin film systems. However, the effects of substrate compliance on the indentation response of compliant substrate systems are not well understood. This paper investigates the effects of the large compliance mismatch between the film and the substrate and of the film thickness for model systems using nanoindentation tests, finite element simulations, and an analytical model based on a classical plate-bending solution. The results showed that for displacements less than the film thickness and for ratio of the substrate to film modulus less than 100. The indentation force-displacement response exhibits a linear relationship that can be predicted accurately by the linear plate-bending model. The effective stiffness depends linearly on the film thickness and also on the substrate and film moduli. For larger displacements, the indentation response exhibits the scaling relationship of the nonlinear plate-bending model.