This article describes the model development and preliminary progress of an on-going research study on the effects of nonlinearities in ocean wave input and power-take-off (PTO) control on wave energy conversion system dynamics and efficiency. The model system employed and progress on recent developments are: (1) nonlinear wave modeling in the ocean, generation and propagation in a wave basin, and (2) nonlinear PTO control algorithm. An overview of the holistic analytical, numerical and experimental research approach/work plan is presented. To provide a simple means for analysis, comparison and performance evaluation, the WEC-Sim numerical platform is used for model implementation and system dynamic simulation. Analytical and numerical predictions of the nonlinear wave fields in a wave basin using the nonlinear Fourier analysis (NLFA) technique and corresponding nonlinear wavemaker theory and a plan for future validation using a comprehensive series of experimental test data as well as ocean wave measurements are described. Efficiency of the nonlinear PTO control and a future evaluation work plan by comparing numerical simulations with results of WEC model test data under corresponding wave conditions of the experimental studies without the presence of the WEC system are also presented.