Worldwide increasing energy demands promote development of environment-friendly energy sources. As consequences, ocean wave is exploited as an ideal energy source to mitigate greenhouse gas emissions. In this paper, a hydraulic energy-storage wave energy conversion system is constructed, and a mathematical model of main components is built for analysis. Control strategies of generator-side and grid-side are defined for the system, where a Vienna rectifier is applied to converter of generator-side. A two-level space vector plane simplified modulation method for Vienna rectifier is designed for the three-level system and a modulation algorithm is detailed, which has lower complexity compared with traditional three-level space vector pulse width modulation (SVPWM) algorithm. An improved adjusting factor method is proposed to solve the potential imbalance of neutral point caused by uneven charging to the upper and lower capacitors in the three-level structure, which optimizes sector division and inhibits the neutral-point potential offset and fluctuation effectively. Using Matlab/Simulink, the intermittent and continuous power conversion modes of the system under different wave conditions are simulated. The results indicate stable operation of the system, feasible topology scheme, modulation algorithm and control strategy, and effective suppression of AC-side harmonics.