The optimal design of hybrid power generation systems (HPGSs) can significantly improve the technical and economic performance of power supply. However, the discrete-time simulation with logical disjunctions involved in HPGS design usually leads to a nonsmooth optimization model, to which well-established techniques for smooth nonlinear optimization cannot be directly applied. This paper casts the HPGS design optimization problem as a multidisciplinary design optimization problem with complementarity constraints, a formulation that introduces a complementarity formulation of the nonsmooth logical disjunction, as well as a time horizon decomposition framework, to ensure a fast local solution. A numerical study of a stand-alone hybrid photovoltaic/wind power generation system is presented to demonstrate the effectiveness of the proposed approach.