Water wave energy is a promising renewable energy source that may alleviate the rising concerns over current resource depletion, but it is rarely exploited due to the lack of efficient energy harvesting technologies. In this work, a hybrid system with a triboelectric nanogenerator (TENG) and an electromagnetic generator (EMG) based on an optimized inner topological structure is reported to effectively harvest water wave energy. The TENG with etched polytetrafluoroethylene films and Cu electrodes utilizing the contact-freestanding mode is designed into a cubic structure, in which the EMG is well hybridized. An integration of TENG and EMG achieves mutual compensation of their own merits, enabling the hybrid system to deliver satisfactory output over a broad range of operation frequency. The output performance of TENG with varied inner topological structures is experimentally and theoretically compared, and a concept is proposed to further clarify the energy conversion efficiency, which should be considered in designing energy harvesting devices. The influences of oscillation frequency, amplitude, and dielectric materials on the output performance of the hybrid system are comprehensively studied on different platforms. Furthermore, the optimum operation frequency ranges for TENG and EMG are concluded. The proposed hybrid nanogenerator renders an effective approach toward large-scale blue energy harvesting over a broad frequency range.