The existing thermal infrared (TIR) ship detection methods may suffer serious performance degradation in the situation of heavy sea clutter. To cope with this problem, a novel ship detection method based on morphological reconstruction and multi-feature analysis is proposed in this paper. Firstly, the TIR image is processed by opening- or closing-based gray-level morphological reconstruction (GMR) to smooth intricate background clutter while maintaining the intensity, shape, and contour features of ship target. Then, considering the intensity and contrast features, the fused saliency detection strategy including intensity foreground saliency map (IFSM) and brightness contrast saliency map (BCSM) is presented to highlight potential ship targets and suppress sea clutter. After that, an effective contour descriptor namely average eigenvalue measure of structure tensor (STAEM) is designed to characterize candidate ship targets, and the statistical shape knowledge is introduced to identify true ship targets from residual non-ship targets. Finally, the dual method is adopted to simultaneously detect both bright and dark ship targets in TIR image. Extensive experiments show that the proposed method outperforms the compared state-of-the-art methods, especially for infrared images with intricate sea clutter. Moreover, the proposed method can work stably for ship target with unknown brightness, variable quantities, sizes, and shapes.