An OTEC (Ocean Thermal Energy Conversion) pilot plant consists of two parts; an OTEC system of main part and a heat reservoir system of sub part. The nonlinear separation control method was applied to the controller design for the OTEC pilot plant. The nonlinear separation models were constructed for the OTEC system and the heat reservoir system. The controller for the OTEC system and the heat reservoir system was designed by using the both nonlinear separation models. A detail simulation study showed that the multi-layer controller for the OTEC pilot plant brought a satisfactory control performance by comparing a conventional PI control.