This paper aims to present an improved bicoherence spectrum (IBS) combined with cyclic modulation spectrum (CMS) and cross-correlation that is suitable for classification of hydrophone signals involving deep learning (DL). First, the proposed feature utilizes the all-phase fast Fourier transform to modify the spectrum leakage caused by CMS; this can be used to detect line spectra with low signal-to-noise ratios (SNRs). Second, the cross-correlation and bispectrum are both exploited to suppress non-periodic line spectra interference from CMS. Based on numerous numerical simulations and experimental verification, compared with CMS and conventional bispectrum, the prominent characteristics of IBS include: detecting higher-precision periodic harmonics without single-line interference, superior robustness under low SNR, and greatly reducing the data redundancy. In addition, to test the performance of IBS for DL application, three deep belief network (DBN)-based classifiers-DBN-softmax, DBN-support vector machine, and DBN-random forest-are introduced and employed for five experimental scenarios (including ships and underwater source). The results indicate that benefiting from DBN pre-training, the IBS classification accuracy of DBN-based models is generally higher than 80%.