Estimating the line spectra of ship-radiated noise is a crucial remote sensing technique for detecting and recognizing underwater acoustic targets. Improving the signal-to-noise ratio (SNR) makes the low-frequency components of the target signal more prominent. This enhancement aids in the detection of underwater acoustic signals using sonar. Based on the characteristics of low-frequency narrow-band line spectra signals in underwater target radiated noise, we propose a dual-stream deep learning network with frequency characteristics transformation (DS_FCTNet) for line spectra estimation. The dual streams predict amplitude and phase masks separately and use an information exchange module to swap learn features between the amplitude and phase spectra, aiding in better phase information reconstruction and signal denoising. Additionally, a frequency characteristics transformation module is employed to extract convolutional features between channels, obtaining global correlations of the amplitude spectrum and enhancing the ability to learn target signal features. Through experimental analysis on ShipsEar, a dataset of underwater acoustic signals by hydrophones deployed in shallow water, the effectiveness and rationality of different modules within DS_FCTNet are verified.Under low SNR conditions and with unknown ship types, the proposed DS_FCTNet model exhibits the best line spectrum enhancement compared to methods such as SEGAN and DPT_FSNet. Specifically, SDR and SSNR are improved by 14.77 dB and 13.58 dB, respectively, enabling the detection of weaker target signals and laying the foundation for target localization and recognition applications.