Abstract: Natural transformation of pesticide residues and transformation of pesticide residues under influence of pulsed electric field were investigated at macromolecular level, and a pesticide residue model was constructed using a meta-cellular automata algorithm to simulate process of pesticide residue degradation by high voltage pulsed electric field to study kinetic changes of pesticide residue degradation．Degradation effect of malathion pesticide residues after electric field intervention was also tested, mass spectra of malathion were obtained by Full scan of gas-mass spectrometer for qualitative analysis of its degradation, and then SIM scan was used for quantitative analysis to calculate and predict degradation rate of different high-voltage pulse action parameters．The maximum difference between degradation model value and real degradation value was 0.0616 μg/mL, and the minimum difference was 0.0003 μg/mL．It could provide a theoretical basis for pesticide residues in fruits and vegetables．