The high-altitude imaging capabilities of Unmanned Aerial Vehicles (UAVs) offer an effective solution for maritime Search and Rescue (SAR) operations. In such missions, the accurate identification of boats, personnel, and objects within images is crucial. While object detection models trained on general image datasets can be directly applied to these tasks, their effectiveness is limited due to the unique challenges posed by the specific characteristics of maritime SAR scenarios. Addressing this challenge, our study leverages the large-scale benchmark dataset SeaDronesSee, specific to UAV-based maritime SAR, to analyze and explore the unique attributes of image data in this scenario. We identify the need for optimization in detecting specific categories of difficult-to-detect objects within this context. Building on this, an anchor box optimization strategy is proposed based on clustering analysis, aimed at enhancing the performance of the renowned two-stage object detection models in this specialized task. Experiments were conducted to validate the proposed anchor box optimization method and to explore the underlying reasons for its effectiveness. The experimental results show our optimization method achieved a 45.8% and a 10% increase in average precision over the default anchor box configurations of torchvision and the SeaDronesSee official sample code configuration respectively. This enhancement was particularly evident in the model’s significantly improved ability to detect swimmers, floaters, and life jackets on boats within the SeaDronesSee dataset’s SAR scenarios. The methods and findings of this study are anticipated to provide the UAV-based maritime SAR research community with valuable insights into data characteristics and model optimization, offering a meaningful reference for future research.