Ship detection in synthetic aperture radar (SAR) imagery faces significant challenges due to the limitations of traditional methods, such as convolutional neural network (CNN) and anchor-based matching approaches, which struggle with accurately detecting smaller targets as well as adapting to varying environmental conditions. These methods, relying on either intensity values or single-target characteristics, often fail to enhance the signal-to-clutter ratio (SCR) and are prone to false detections due to environmental factors. To address these issues, a novel framework is introduced that leverages the detection transformer (DETR) model along with advanced feature fusion techniques to enhance ship detection. This feature enhancement DETR (FEDETR) module manages clutter and improves feature extraction through preprocessing techniques such as filtering, denoising, and applying maximum and median pooling with various kernel sizes. Furthermore, it combines metrics like the line spread function (LSF), peak signal-to-noise ratio (PSNR), and F1 score to predict optimal pooling configurations and thus enhance edge sharpness, image fidelity, and detection accuracy. Complementing this, the weighted feature fusion (WFF) module integrates polarimetric SAR (PolSAR) methods such as Pauli decomposition, coherence matrix analysis, and feature volume and helix scattering (Fvh) components decomposition, along with FEDETR attention maps, to provide detailed radar scattering insights that enhance ship response characterization. Finally, by integrating wave polarization properties, the ability to distinguish and characterize targets is augmented, thereby improving SCR and facilitating the detection of weakly scattered targets in SAR imagery. Overall, this new framework significantly boosts DETR’s performance, offering a robust solution for maritime surveillance and security.