In order to study the mechanism of electrical discharge machining(EDM), the energy distribution of cathode and anode was calculated based on photon emission. The matter waves of positive ion and electron were firstly obtained and knowledge was got that the positive ion mainly moved in vibration and produced photon emission in discharge channel, and that the electron mainly moved in diffraction and produced photon emission at anode. The photon emission was assumed equal probability, and several equations had been attained about heat density, heat and average heat density, and a newly explanation was submitted that large polar action expressed when using small duration charge, and small polar action expressed when using large duration charge. At last, the affection of this mechanism was applied to micro EDM, finish machining and rough machining, showed that small duration charge matched with normal polarity (work piece to positive electrode) and compacting discharge channel which could guarantee the precision, and that large duration charge matched with reversed polarity (work piece to negative electrode) and no need to compact discharge channel which could guarantee machining efficiency and surface quality.