This paper proposes a novel online control method for Hybrid Active Power Filter with Injection Circuit (IHAPF). It includes two closed-control loops. The lower closed-control loop contains a conventional PI controller and IHAPF model, while the upper closed-control loop is composed of predictive neural network model, optimization adjustor using generalized predictive control criterion (GPC) and IHAPF model. The purpose of the upper closed-control loop is to find a set of optimal PI parameters for the lower closed-control loop. Compared to the conventional PI control method, the simulation and experimental results show that the proposed control method has the advantages of shorter response time, able to online control very well and very effective in reducing harmonics.