According to the feature that the underwater target radiated noise contains high intensive and stable line spectrum, a weighted line spectrum detection method based on the instantaneous phase’s variance is proposed with regard to the problem of unknown line spectrum detection. This method utilizes the characteristic that the instantaneous phase of target line spectral frequency unit being stable, and the instantaneous phase of noise frequency unit being random, to weight each frequency unit by the instantaneous phase variance, and can further restrain the background noise energy disturbances and enhance the Signal to Noise Ratio (SNR) gain of the target line spectrum detection, and achieves detecting unknown line spectrum of underwater target radiated noise. The theoretical analysis and experimental results both show that this method can well enhance the target line spectral energy and restrain the background noise energy, and has the capacity of improving SNR. It has better application prospects to the detection and identification areas of anti-complex channel.