Accurate and timely cotton-field mapping is essential for irrigation management, water resource allocation, and regional yield assessment in arid irrigated agroecosystems. However, existing deep-learning-based crop mapping approaches generally lack interpretability and often exhibit performance variability across phenological stages, thereby limiting their reliability for operational deployment. To address these limitations, we developed an interpretable semantic segmentation framework for cotton mapping in the Wei-Ku Oasis, Xinjiang, China, under multi-source remote sensing conditions. The proposed model integrates Sentinel-2 surface reflectance, Sentinel-1 VV/VH backscatter, DEM, vegetation indices, and GLCM texture features. By incorporating a receptive-field enhancement mechanism together with an embedded feature-attribution module, the framework enables importance estimation of multi-source predictors within the network architecture, thereby providing intrinsic model interpretability. Under a unified training and evaluation protocol, the proposed model achieved an mIoU of 85.62% and an F1-score of 92.96% on the test set, outperforming U-Net, DeepLabV3+, and SegFormer baselines. Monthly classification results indicated that August provided the most discriminative acquisition window (mIoU = 85.54%, F1 = 92.83%), while June–July also maintained high recognition accuracy. Feature attribution results indicate that the importance of different predictors varies across phenological stages: Sentinel-2 red-edge bands remained highly influential throughout the growing season, NDVI/EVI exhibited increased contributions during June–August, SAR VH showed relatively higher importance during peak canopy development, and DEM maintained stable information contribution across all stages. Cross-year and cross-region experiments further demonstrated the model’s generalization capability, achieving an mIoU of 82.81% in same-region cross-year evaluation and 74.56% under cross-region transfer. Overall, the proposed segmentation framework improves classification accuracy while explicitly modeling and quantifying feature importance, providing a methodological reference for cotton-field mapping and acquisition timing selection in arid irrigated regions.