To more effectively detect small ships, in this article, a novel region-based polarimetric covariance difference matrix [RP] is put forward, which mainly consists of two stages. Briefly speaking, in the first stage, a new pixel representation way is proposed to depict the spatial characteristics of pixel, through which the difference information related to pixel’s local region is calculated as well. In the second stage, the global region difference information of pixel is computed. Finally, we construct [RP] via fusing these two different kinds of information together with a balance factor . Meanwhile, considering that the backscattering energy of ships is useful for ship detection, a new intensity-driven polarimetric notch filter (ID-PNF _RP ) is also derived from [RP]. Three different datasets are adopted to evaluate the effectiveness of [RP] and ID-PNF _RP . Experimental results show that: 1) compared with the polarimetric covariance matrix [ ] and the polarimetric covariance difference matrix [ ], [RP] is more suitable for ship detection and 2) compared with the original geometrical perturbation-polarimetric notch filter (GP-PNF) and the total power detector SPAN, the proposed method ID-PNF _RP can better detect small ships with greater figure of merit (FoM) and target-to-clutter ratio (TCR) values.