Abstract: The frequency shifts of acoustic intensity interference pattern could be used to monitor the internal waves. But there wasn't an effective method to extract the frequency shift line from the experiment data because of the huge fluctuation of acoustic mode's amplitude. An improved method for the extraction of frequency shift line from experiment data was proposed. With the help of mode filtering the method used the correlation function to extract the frequency shift line from the difference of the phase angles of the modes. The extracted frequency shift line has great similarity with the thermoeline depth variance caused by internal waves, which is proved by the experiment in Yellow Sea 2011. This method could preserve the frequency shifts caused by the change of acoustic modal phase difference, while at the same time restrain the disturbance of the acoustic mode amplitude' fluctuation, but needed a fine layout of the receiver line array to ensure the mode separation of the normal modes.