The proper integration of wind power-driven grids relies heavily on a reliable balance between electricity production and demand. Therefore, accurate prediction is essential for planning and efficient operation of wind power systems to ensure their continuous supply. However, increasingly severe power quality disturbance (PQD) constantly disturbs this equilibrium, which affects the accuracy of wind power prediction to a large extent. For this purpose, this paper developed a novel optimization methodology to improve wind power prediction accuracy considering micro PQD dimension reduction and elimination for wind-storage integrated systems. A novel idea has been presented in this optimization methodology to eliminate the barrier of PQD and wind power prediction. In the micro aspect, a PQD dimension reduction and elimination strategy based on dynamic mode decomposition (DMD) and Wiener Filter (WF) is proposed to eliminate the autonomy of PQD. This elimination of autonomy allows the WF to get a higher signal-to-noise ratio (SNR). In the macro aspect, this paper takes PQD of different complexity into full consideration, and compares their effects on improving wind power prediction accuracy based on deep learning-based approaches. Through the experimental verification, it is confirmed that the proposed DMD-WF optimization method has demonstrated an effective dimension reduction and elimination of PQD. Moreover, it is found that the proposed PQD optimization method contributes to improve the deep learning-based prediction accuracy when PQD is more complex. The proposed methodology creates a novel perspective to improve the short-term wind power prediction accuracy, which provides a theoretical and methodological guidance for future development of large-scale integrated wind-storage systems.