Accurate quantification of field-grown rice seedlings is essential for evaluating yield potential and guiding precision field management. Unmanned aerial vehicle (UAV)-based remote sensing, with its high spatial resolution and broad coverage, provides a robust basis for accurate seedling detection and population density estimation. However, in previous studies, UAVs were typically employed at relatively low altitudes, which provided high-resolution imagery and facilitated seedling recognition but limited efficiency. To enable large-area monitoring, higher flight altitudes are required, which reduces image resolution and adversely affects rice seedling recognition accuracy. In this study, UAVs were flown at a height of 30 m, and the resulting lower-resolution imagery, combined with the small size of seedlings, their dense spatial distribution, and the complex field background, necessitated algorithmic improvements for accurate detection. To address these challenges, we propose an enhanced You Only Look Once version 8 nano (YOLOv8n)-based detection model specifically designed to improve seedling recognition under high-altitude UAV imagery. The model incorporates an improved Bidirectional Feature Pyramid Network (BiFPN) for multi-scale feature fusion and small-object detection, a Global-to-Local Spatial Aggregation (GLSA) module for enriched spatial context modeling, and a Content-Guided Attention Fusion (CGAFusion) module to enhance discriminative feature learning. Experiments on high-altitude UAV imagery demonstrate that the proposed model achieves an mAP@0.5 of 94.7%, a precision of 91.0%, and a recall of 91.2%, representing a 2.3% improvement over the original YOLOv8n. These results highlight the model’s innovation in handling high-altitude UAV imagery for large-area rice seedling detection, demonstrating its effectiveness and practical potential under complex field conditions.