Due to the strong speckle noise caused by the seabed reverberation which makes it difficult to extract discriminating and noiseless features of a target, recognition and classification of underwater targets using side-scan sonar (SSS) images is a big challenge. Moreover, unlike classification of optical images which can use a large dataset to train the classifier, classification of SSS images usually has to exploit a very small dataset for training, which may cause classifier overfitting. Compared with traditional feature extraction methods using descriptors—such as Haar, SIFT, and LBP—deep learning-based methods are more powerful in capturing discriminating features. After training on a large optical dataset, e.g., ImageNet, direct fine-tuning method brings improvement to the sonar image classification using a small-size SSS image dataset. However, due to the different statistical characteristics between optical images and sonar images, transfer learning methods—e.g., fine-tuning—lack cross-domain adaptability, and therefore cannot achieve very satisfactory results. In this paper, a multi-domain collaborative transfer learning (MDCTL) method with multi-scale repeated attention mechanism (MSRAM) is proposed for improving the accuracy of underwater sonar image classification. In the MDCTL method, low-level characteristic similarity between SSS images and synthetic aperture radar (SAR) images, and high-level representation similarity between SSS images and optical images are used together to enhance the feature extraction ability of the deep learning model. Using different characteristics of multi-domain data to efficiently capture useful features for the sonar image classification, MDCTL offers a new way for transfer learning. MSRAM is used to effectively combine multi-scale features to make the proposed model pay more attention to the shape details of the target excluding the noise. Experimental results of classification show that, in using multi-domain data sets, the proposed method is more stable with an overall accuracy of 99.21%, bringing an improvement of 4.54% compared with the fine-tuned VGG19. Results given by diverse visualization methods also demonstrate that the method is more powerful in feature representation by using the MDCTL and MSRAM.