To maximize the generated output power under random waves, the control strategy of maximum power point tracking (MPPT) is incorporated in point-absorbing type wave energy converter (WEC) system. However, due to the influence of mutative wave conditions, the curve of the maximum average power appears in multiple peaks, adding complexity to the tracking process. This paper proposes a new MPPT control technique for a wave power generation system, by using the flower pollination algorithm (FPA) instead of the conventional hill-climbing method. Compared with the hill-climbing method, this method has advantages of achieving a smaller peak-to-average ratio and capturing the more average power under the same sea state. The verification has been carried out through the simulations and the experimental results on a lab test bench.