The precise extraction of winter wheat planting structure holds significant importance for food security risk assessment, agricultural resource management, and governmental decision-making. This study proposed a method for extracting the winter wheat planting structure by taking into account the growth phenology of winter wheat. Utilizing the fitting effect index, the optimal Savitzky–Golay (S–G) filtering parameter combination was determined automatically to achieve automated filtering and reconstruction of NDVI time series data. The phenological phases of winter wheat growth was identified automatically using a threshold method, and subsequently, a model for extracting the winter wheat planting structure was constructed based on three key phenological stages, including seeding, heading, and harvesting, with the combination of hierarchical classification principles. A priori sample library was constructed using historical data on winter wheat distribution to verify the accuracy of the extracted results. The validation of fitting effect on different surfaces demonstrated that the optimal filtering parameters for S–G filtering could be obtained automatically by using the fitting effect index. The extracted winter wheat phenological phases showed good consistency with ground-based observational results and MOD12Q2 phenological products. Validation against statistical yearbook data and the proposed priori knowledge base exhibited high statistical accuracy and spatial precision, with an extracting accuracy of 94.92%, a spatial positioning accuracy of 93.26%, and a kappa coefficient of 0.9228. The results indicated that the proposed method for winter wheat planting structure extracting can identify winter wheat areas rapidly and significantly. Furthermore, this method does not require training samples or manual experience, and exhibits strong transferability.