The invention provides a mass spectrometry analysis method and a mass spectrometry system, including: a first sample separation step, separating a sample by a first sample separation device to obtain first isolates; a second sample separation step, introducing ionized first isolates into a second sample separation device for further separation based on a difference in ion mobility to obtain second isolates; and a mass spectrometry analysis step, performing mass spectrometry detection at least on daughter ions obtained from dissociation of the second isolates; in the second sample separation step, the second sample separation device operates in a filter mode, and screens out and releases ions having ion mobility within a specified range from received second isolates. The mass spectrometry analysis method can improve the dynamic range of mass spectrometry analysis.