The invention belongs to the technical field of mass spectrometry testing, and particularly provides an ion trap low mass cutoff tandem mass spectrometry method. The method comprises three phases of ion selected isolation, collision induced dissociation and mass analysis. In the phase of collision induced dissociation, frequency of a digital square wave power is scanned, linear scanning is performed from low frequency to high frequency, and certain excitation square wave voltage is simultaneously loaded in the implementation process so that excitation and dissociation of an analyzed parent ion can be realized, and the low mass fragment ion products of the parent ion can be detected. The advantages of the method are that hardware and equipment do not need to be changed, and frequency change of the digital square wave power supply can be realized by software control so that the main difficulties of low mass detection by a conventional ion trap mass spectrometer in the tandem mass spectrometry process can be solved; besides, tandem mass spectrometry dissociation efficiency of the ion trap mass spectrometer is further enhanced, fragment ion information is enriched and analysis of the structure of the parent ion is facilitated so that the performance and application field of the ion trap mass spectrometer can be enhanced.