The present invention provides a method and a system for detecting and distinguishing a passive synthetic aperture target signal, wherein the method comprises the following steps: step 101) constructing a motion doppler receiving model for a target signal under motion of a towed array sonar; step 102) respectively performing cross correlation averaging on target signals which are received by a hydrophone at an overlapping part on spatial position according to a passive synthetic aperture sonar algorithm when the array performs two successive motions in a fixed time interval, and then performing frequency domain wave beam forming treatment on the target signals which are received by array elements at different time periods; step 103) performing energy integration on the output sub-frequency-bands after forming of the frequency domain wave beam for obtaining wave beam output of each time interval; step 104) performing phase estimation on time delay and spatial position movement according to the doppler receiving model, and acquiring a phase correction factor according to the phase estimation; and step 105) compensating the wave beam output through each phase correction factor of time interval, and performing cross combined accumulation on the compensated wave beam output and realizing detection on the target through a time orientation process map.