Orthogonal chirp division multiplexing (OCDM) offers a promising modulation technology for shallow water underwater acoustic (UWA) communication systems due to multipath fading resistance and Doppler resistance. To handle the various channel distortions and interferences, obtaining accurate channel state information is vital for robust and efficient shallow water UWA communication. In recent years, deep learning has attracted widespread attention in the communication field, providing a new way to improve the performance of physical layer communication systems. In this paper, the pilot-based channel estimation is transformed into a matrix completion problem, which is mathematically equivalent to the image super-resolution problem arising in the field of image processing. Simulation results show that the deep learning-based method can improve the channel distortion, outperforming the equalization performed by traditional estimator, the performance of Bit Error Rate is improved by 2.5 dB compared to the MMSE method in OCDM system. At the 7.5 to 20 dB region, it achieves better bit error rate performance than OFDM systems, and the bit error rate is reduced by approximately 53% compared to OFDM when the SNR value is 20, which is very useful in shallow water UWA channels with multipath extension and severe time-varying characteristics.