Abstract: Higher reliable numerical calculation model of ion trajectory in quadrupole mass spectrometry was explained from a theoretical point of view in this paper. Combining with the actual needs of instrument study, this paper focuses on the quadrupole mass spectrometer ion trajectory simulation system design and implementation. The problems of high order fields, dipole excitation and space charge effects in quadrupole ion trap were simulated by this ion trajectory simulator. And the results demonstrate the effectiveness of the simulation system.