The accurate estimation of corn canopy structure and light conditions is essential for effective crop management and informed variety selection. This study introduces CCSNet, a deep learning-based semantic segmentation model specifically developed to extract fractional coverages of soil, illuminated vegetation, and shaded vegetation from high-resolution corn canopy images acquired by UAVs. CCSNet improves segmentation accuracy by employing multi-level feature fusion and pyramid pooling to effectively capture multi-scale contextual information. The model was evaluated using Pixel Accuracy (PA), mean Intersection over Union (mIoU), and Recall, and was benchmarked against U-Net, PSPNet and UNetFormer. On the test set, CCSNet utilizing a ResNet50 backbone achieved the highest accuracy, with an mIoU of 86.42% and a PA of 93.58%. In addition, its estimation of fractional coverage for key canopy components yielded a root mean squared error (RMSE) ranging from 3.16% to 5.02%. Compared to lightweight backbones (e.g., MobileNetV2), CCSNet exhibited superior generalization performance when integrated with deeper backbones. These results highlight CCSNet’s capability to deliver high-precision segmentation and reliable phenotypic measurements. This provides valuable insights for breeders to evaluate light-use efficiency and facilitates intelligent decision-making in precision agriculture.