The number of seedlings is an important indicator that reflects the size of the wheat population during the seedling stage. Researchers increasingly use deep learning to detect and count wheat seedlings from unmanned aerial vehicle (UAV) images. However, due to the small size and diverse postures of wheat seedlings, it can be challenging to estimate their numbers accurately during the seedling stage. In most related works in wheat seedling detection, they label the whole plant, often resulting in a higher proportion of soil background within the annotated bounding boxes. This imbalance between wheat seedlings and soil background in the annotated bounding boxes decreases the detection performance. This study proposes a wheat seedling detection method based on a local annotation instead of a global annotation. Moreover, the detection model is also improved by replacing convolutional and pooling layers with the Space-to-depth Conv module and adding a micro-scale detection layer in the YOLOv5 head network to better extract small-scale features in these small annotation boxes. The optimization of the detection model can reduce the number of error detections caused by leaf occlusion between wheat seedlings and the small size of wheat seedlings. The results show that the proposed method achieves a detection accuracy of 90.1%, outperforming other state-of-the-art detection methods. The proposed method provides a reference for future wheat seedling detection and yield prediction.