The invention relates to the technical field of mass spectrometry and provides an ion dissociation method based on a quadrupole rod-ion trap tandem mass spectrometer. A sample is ionized by an electrospray ion source, ions with a set mass-to-charge ratio are screened out from ionized ions by utilizing a quadrupole rod to enter an ion trap, the ions are dissociated by the ion trap, and dissociatedfragment ions are stored in the ion trap, wherein two processes of screening the target ions by the quadrupole rod and dissociating the ions by the ion trap are carried out at the same time. Differentfrom a traditional dissociation operation which occurs after an ion gate is closed, according to the method, a dissociation operation is applied to the ion trap while the target ions are screened bythe quadrupole rod, so that the target ions and impurity ions with similar mass-to-charge ratios are dissociated immediately when entering the ion trap, the dissociation of the target ions and the capture of the fragment ions are not interfered by the impurity ions, and the analysis accuracy is remarkably improved; meanwhile, the dissociation operation does not need to be carried out in an additional time sequence, so that the operation time is saved.