Synthetic aperture radar (SAR) is an essential tool for monitoring and managing maritime traffic and ensuring safety. It is particularly valuable because it can provide surveillance in all weather conditions. Ship wake detection has attracted considerable attention in offshore management as it has potential for widespread use in ship positioning and motion parameter inversion, surpassing conventional ship detection methods. Traditional wake detection methods depend on linear feature extraction through image transformation processing techniques, which are often ineffective and time-consuming when applied to large-scale SAR data. Conversely, deep learning (DL) algorithms have been infrequently utilized in wake detection and encounter significant challenges due to the complex ocean background and the effect of the sea state. In this study, we propose a lightweight rotating target detection network designed for detecting ship wakes under various sea states. For this purpose, we initially analyzed the features of wake samples across various frequency domains. In the framework, a YOLO structure-based deep learning is implemented to achieve wake detection. Our network design enhances the YOLOv8’s structure by incorporating advanced techniques such as deep separation convolution and combined frequency domain–spatial feature extraction modules. These modules are used to replace the usual convolutional layer. Furthermore, it integrates an attention technique to extract diverse features. By conducting experiments on the OpenSARWake dataset, our network exhibited outstanding performance, achieving a wake detection accuracy of 66.3% while maintaining a compact model size of 51.5 MB and time of 14 ms. This model size is notably less than the existing techniques employed for rotating target detection and wake detection. Additionally, the algorithm exhibits excellent generalization ability across different sea states, addressing to a certain extent the challenge of wake detection being easily influenced by varying sea states.