High-rise pile cap foundations are generally used to support offshore wind turbines or sea-crossing bridges. They endure complex wave loads due to the interaction of free surface and the cap. An additional pressure increment has been found under the cap when free surface impinges the cap bottom. This additional pressure changes the wave loads on the piles under the cap compared with the case without the cap. In the present paper, we investigate the effects of the cap bottom elevation on the wave loads of the piles under the cap by using fully nonlinear numerical simulations. Based on parameters of waves and the structure used in Donghai Bridge Wind Farm, China, we simulate a number of cases with different cap bottom elevation to explore its influence on wave loads of the piles under the cap. We find that the influence is of significance and requires enough attention.