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In order to solve the problem of harmonic waves caused by battery energy storage (BES) and distributed generation (DG) inverters in an active distribution network, an intelligent optimal dispatching method based on a modified flower pollination algorithm (MFPA) is proposed. Firstly, the active distribution network dispatching model considering the power quality (PQ) problem caused by BES and DG is proposed. In this model, the objective function considers the additional network loss caused by a harmonic wave, as well as the constraints of the harmonic wave and voltage unbalance. Then, the MFPA is an improvement of a flower pollination algorithm (FPA). Because the MFPA has the characteristics of higher solution accuracy and better convergence than the FPA and it is not easy to fall into local optimal, the MFPA is used to solve the proposed model. Finally, simulation experiments are carried out on IEEE 37 bus and IEEE 123 bus systems, respectively. The experimental results show that this method can achieve satisfactory power quality while optimizing the total active power loss of the branch. The comparative experimental results show that the developed algorithm has better convergence than the FPA.