The traditional threshold setting method of multi beam sonar multiple detection technology is effective for the detection of multiple echoes with the same beam amplitude. When the echo amplitude is different, the conventional threshold setting method is difficult to adapt and adjust. To address this issue, a joint weighting method based on instantaneous frequency variance and spectral characteristics is proposed to weight the echo amplitude. The instantaneous frequency variance of the echo signal is obtained by using the characteristic that the phase of the echo signal is regular. The spectral characteristics of the signal are analyzed to obtain the equivalent bandwidth of the echo signal. Using the characteristics that the obtained equivalent bandwidth value and the instantaneous frequency variance value are very low or even close to 0, the echo signal of weak target submerged by strong target signal is highlighted, which is convenient for the simultaneous detection of strong and weak targets and improves the detection ability of targets. Computer simulation results show that after joint weighting, the relative amplitude of strong and weak targets is increased by nearly 30%, and the detection ability is improved. Through the field test data processing results, it can be found that the target echo detection ability after instantaneous frequency variance and spectral feature weighting processing has been significantly improved.