In Underwater Acoustic Target Recognition (UATR), accurately extracting spectral lines from time–frequency spectra in complex ocean environments faces three critical challenges: low-frequency spectral confusion, line spectrum and noise mixture, and a computational efficiency vs. performance trade-off. To address these, we propose a deep learning-integrated framework based on application-oriented integration and adaptation of established techniques tailored to the underwater acoustic domain. The framework consists of the following: (1) the Line Spectrum Separation Network (LSS-Net), which integrates a Time–Frequency Joint LSTM and a Temporal Gated Cross-Attention (TGCA) module within an encoder–decoder architecture adapted for high-resolution underwater acoustic time–frequency spectra; (2) a physics-informed signal simulation approach that realistically models Doppler frequency drift and intensity fluctuations; and (3) a Peak-Tracking Line Extractor (PTLE) algorithm that leverages underwater acoustic-specific temporal constraints. The proposed framework achieves an MOTA of 0.89 on simulated data and 0.52 on real sea trial data, outperforming existing methods by 0.06-2.14 in MOTA and significantly suppressing high-resolution background noise.