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This paper proposes a multi-scale rotation-invariant haar-like (MSRI-HL) feature integrated convolutional neural network (MSRIHL-CNN)-based ship detection algorithm of the multiple-target environment in synthetic aperture radar (SAR) imagery. Usually, ship detection includes preprocessing, prescreening, discrimination, and classification. Among them, prescreening and discrimination are the most two important stages so that they catch great intention. Based on our previous work, we propose a truncated-clutter-statistics-based joint, constant false alarm rate (CFAR) detector (TCS-JCFAR) for ship target prescreening in the multiple-target environment. TCS-JCFAR greatly enhances the prescreening rate in the multiple-target environment while achieving a low observed FAR. In the discrimination stage, conventional CNN extracts the deep features (high-level features); however, it will lose the local texture and edge information (low-level features) which are of great significance for target discrimination. Hence, the MSRI-HL features are used to represent the multi-scale, rotation-invariant texture, and edge information that conventional CNN fails to capture. The extracted low-level MSRI-HL features and the high-level deep features are optimally fused to a multi-layered feature vector. Finally, the multi-layered feature vector is fed into a typical support vector machine (SVM) classifier for ship target discrimination. The proposed MSRIHL-CNN combines the low-level texture and edge features and the high-level deep features; moreover, they are optimally fused to fully represent the ship targets. Undoubtedly, MSRIHL-CNN has better discrimination performance. The superiority of the proposed TCS-JCFAR-based prescreener and MSRIHL-CNN-based discriminator is validated on the Chinese Gaofen-3 SAR imagery.