Ship detection under cloudy and foggy conditions is a significant challenge in remote sensing satellite applications, as cloud cover often reduces contrast between targets and backgrounds. Additionally, ships are small and affected by noise, making them difficult to detect. This paper proposes a Cloud Removal and Target Detection (CRTD) network to detect small ships in images with thin cloud cover. The process begins with a Thin Cloud Removal (TCR) module for image preprocessing. The preprocessed data are then fed into a Small Target Detection (STD) module. To improve target–background contrast, we introduce a Target Enhancement module. The TCR and STD modules are integrated through a dual-stage supervision network, which hierarchically processes the detection task to enhance data quality, minimizing the impact of thin clouds. Experiments on the GaoFen-4 satellite dataset show that the proposed method outperforms existing detectors, achieving an average precision (AP) of 88.9%.