Offshore wind and tides are massive sources of sustainable energy. Simulation-based design has the potential for groundbreaking achievements of offshore energy harvesting structures, such as offshore floating wind turbines and tidal stream turbines. There are many engineering challenges associated with the mechanics of these energy harvesting devices, both on the structural mechanics and fluid mechanics sides, which make the analysis and modeling of these machines quite difficult, especially in harsh ocean environment. This dissertation will focus on the efforts to address some of these challenges through advanced free-surface fluid-structure interaction (FSI) simulations. In this dissertation, a novel computational free-surface FSI framework using level-set method, finite element and isogeometric analysis is developed. Considering geometry modeling, aerodynamics, hydrodynamics, free-surface and structural mechanics simultaneously, this formulation enables the simulations of the interaction between free-surface flows and large scale offshore structures with great efficiency, accuracy and robustness. This framework has been applied on a wide range of challenging problems in civil, marine/ocean and mechanical engineering, such as ocean waves, offshore floating wind turbines, tidal energy and bio-inspired aquatic sports equipment.