Underwater target recognition remains a challenging task due to the complex and changeable environment. There have been a huge number of methods to deal with this problem. However, most of them fail to hierarchically extract deep features. In this paper, a novel deep learning framework for underwater target classification is proposed. First, instead of extracting features relying on expert knowledge, sparse autoencoder (AE) is utilized to learn invariant features from the spectral data of underwater targets. Second, stacked autoencoder (SAE) is used to get high-level features as a deep learning method. At last, the joint of SAE and softmax is proposed to classify the underwater targets. Experiment results with the received signal data from three different targets on the sea indicated that the proposed approach can get the highest classification accuracy compared with support vector machine (SVM) and probabilistic neural network (PNN).