The mechanism of olefin elimination in the process of methanol-to-olefins (MTO) over a series of zeolites like HZSM-5, HMOR, HBEA, and HMCM-22 was investigated by DFT-D calculations, which is a crucial step that controls the MTO product distribution. The results demonstrate that the manners of olefin elimination are related to the pore structure of zeolite catalyst and the interaction between proton transfer reagent (water or methanol) and zeolite acidic framework. The indirect spiro mechanism is preferable to the direct mechanism over HMOR, HBEA, and HMCM-22 zeolites with large pores, as suggested by the energy barrier of rate-determining step and the potential energy surface (PES), but is unfavorable over HZSM-5 with medium-sized pores due to the steric hindrance of spiro intermediates. Over various zeolites, water and methanol perform differently in proton transfer to form the spiro intermediates; over HMOR and HBEA with strong acidity, water is superior to methanol in promoting propene elimination, whereas over HMCM-22 with relatively weaker acidity, methanol is more favorable as a proton transfer reagent.