The particle swarm optimization (PSO) algorithm has low probability in searching global optimization and premature convergence in the maximum power point tracking (MPPT) control of the wave energy generation system. A novel simulated annealing particle swarm optimization (SAPSO) algorithm was proposed to solve the problem of the traditional PSO. When the speed and position of each particle were updated with SAPSO, the replacement value of the global maximum from all particles was confirmed by comparing the fitness of each particle of the current temperature and the random number value. As a result, the new algorithm could escape local maximum at the premature convergence and quickly discover global optimum solution. The simulation results showed that this novel algorithm could make the wave energy generation system effectively avoid the local optimization and fast achieve global MPPT control. The capture rate of wave energy was improved.