Rapeseed mapping is crucial for refined agricultural management and food security. However, existing remote sensing-based methods for rapeseed mapping in Southwest China are severely limited by insufficient training samples and persistent cloud cover. To address the above challenges, this study presents an automatic rapeseed mapping framework that integrates multi-source remote sensing data fusion, automated sample generation, and deep learning models. The framework was applied in Santai County, Sichuan Province, Southwest China, which has typical topographical and climatic characteristics. First, MODIS and Landsat data were used to fill the gaps in Sentinel-2 imagery, creating time-series images through the object-level processing version of the spatial and temporal adaptive reflectance fusion model (OL-STARFM). In addition, a novel spectral phenology approach was developed to automatically generate training samples, which were then input into the improved TS-ConvNeXt ECAPA-TDNN (NeXt-TDNN) deep learning model for accurate rapeseed mapping. The results demonstrated that the OL-STARFM approach was effective in rapeseed mapping. The proposed automated sample generation method proved effective in producing reliable rapeseed samples, achieving a low Dynamic Time Warping (DTW) distance (<0.81) when compared to field samples. The NeXt-TDNN model showed an overall accuracy (OA) of 90.12% and a mean Intersection over Union (mIoU) of 81.96% in Santai County, outperforming other models such as random forest, XGBoost, and UNet-LSTM. These results highlight the effectiveness of the proposed automatic rapeseed mapping framework in accurately identifying rapeseed. This framework offers a valuable reference for monitoring other crops in similar environments.