Wheat and corn are two major food crops in Xinjiang. However, the spectral similarity between these crop types and the complexity of their spatial distribution has posed significant challenges to accurate crop identification. To this end, the study aimed to improve the accuracy of crop distribution identification in complex environments in three ways. First, by analysing the kNDVI and EVI time series, the optimal identification window was determined to be days 156-176-a period when wheat is in the grain-filling to milk-ripening phase and maize is in the jointing to tillering phase-during which, the strongest spectral differences between the two crops occurs. Second, principal component analysis (PCA) was applied to Sentinel-2 data. The top three principal components were extracted to construct the input dataset, effectively integrating visible and near-infrared band information. This approach suppressed redundancy and noise while replacing traditional RGB datasets. Finally, the Convolutional Block Attention Module (CBAM) was integrated into the U-Net model to enhance feature focusing on key crop areas. An improved Atrous Spatial Pyramid Pooling (ASPP) module based on deep separable convolutions was adopted to reduce the computational load while boosting multi-scale context awareness. The experimental results showed the following: (1) Wheat and corn exhibit obvious phenological differences between the 156th and 176th days of the year, which can be used as the optimal time window for identifying their spatial distributions. (2) The method proposed by this research had the best performance, with its mIoU, mPA, F1-score, and overall accuracy (OA) reaching 83.03%, 91.34%, 90.73%, and 90.91%, respectively. Compared to DeeplabV3+, PSPnet, HRnet, Segformer, and U-Net, the OA improved by 5.97%, 4.55%, 2.03%, 8.99%, and 1.5%, respectively. The recognition accuracy of the PCA dataset improved by approximately 2% compared to the RGB dataset. (3) This strategy still had high accuracy when predicting wheat and corn yields in Qitai County, Xinjiang, and had a certain degree of generalisability. In summary, the improved strategy proposed in this study holds considerable application potential for identifying the spatial distribution of wheat and corn in arid regions.