For the purpose of improving the accuracy of underwater acoustic target recognition with only a small number of labeled data, we proposed a novel recognition method, including 4 steps: pre-processing, pre-training, fine-tuning and recognition. The 4 steps can be explained as follows: (1) Pre-processing with Resonance-based Sparsity Signal Decomposition (RSSD): RSSD was firstly utilized to extract high-resonance components from ship-radiated noise. The high-resonance components contain the major information for target recognition. (2) Pre-training with unsupervised feature-extraction: we proposed a one-dimensional convolution autoencoder-decoder model and then we pre-trained the model to extract features from the high-resonance components. (3) Fine-tuning with supervised feature-separation: a supervised feature-separation algorithm was proposed to fine-tune the model and separate the extracted features. (4) Recognition: classifiers were trained to recognize the separated features and complete the recognition mission. The unsupervised pre-training autoencoder-decoder can make good use of a large number of unlabeled data, so that only a small number of labeled data are required in the following supervised fine-tuning and recognition, which is quite effective when it is difficult to collect enough labeled data. The recognition experiments were all conducted on ship-radiated noise data recorded using a sensory hydrophone. By combining the 4 steps above, the proposed recognition method can achieve recognition accuracy of 93.28%, which sufficiently surpasses other traditional state-of-art feature-extraction methods.