Abstract: The Geant4 was used to construct the head and irradiation conditions of 6 MV medical accelerator. The measurement data in the water phantom were compared to ensure the constructed model correct. Phase space files of different fields and different levels were obtained by simulating the process of particle transporting of the accelerator. The positron and annihilation photon were as indicator, and the effect of fields and components of the accelerator head on the production of electron-pair was studied by analyzing those files. The influence of electron-pair effect on accelerator beam and energy deposited in the phantom was simulated. The results show that the smaller the field is, the more the production of electron-pair is. The production of electron-pair is obvious when beam passes through target, flatten filter and secondary collimator, and it is especially obvious to secondary collimator. The electron-pair effect makes contamination electron increase about 4%, beam’s average energy lower, beam’s particle angular distribution more dispersed and doses of surface of phantom and outside fields increase.