In this paper, the peak migration line of cross-correlation output is utilized to discriminate the depth of an underwater acoustic source in shallow water environment with a negative thermocline through studying the modal arrival structure of the source at different depths. The discrimination can be done according to the position of the migration line when the cross-correlation delay is zero since the type of dominant normal mode is determined by the depth of the source. Firstly, using the beam output of a vertical linear array and the received signal of a single array element to do cross-correlation processing, a two-dimensional intensity image of cross-correlation delay versus elevation angle is obtained. Then, the peaks in the angle domain at different delays can be extracted from the image. The cross-correlation peak migration line can be achieved by piecewise linear fitting which is divided into two parts corresponding to the delay being less than or equal to zero and the delay being more than zero, respectively. Finally, the source depth is determined by the position of the curve where the cross-correlation time delay is zero. Theoretical analysis shows that the migration line is little influenced by the sound velocity profile (SVP) varying with depth, the discrimination threshold is determined by the lower-order normal modes, the identification region is determined by the thickness and depth of the thermocline and the higher strength of the thermocline is instrumental in distinguishing. The numerical results and the experimental results prove the method's effectiveness which can be implemented without SVP details or mode separation, or source movement.