Methanol-to-olefin (MTO) reaction was studied over MWW zeolite with independently developed two pores (circular and straight) and MFI zeolite with intercrossed sinusoidal and straight pores in order to investigate the effect of pore structure on their catalytic behavior. MWW and MFI zeolites with similar acidity exhibited commonly high conversion and slow deactivation in the MTO reaction, but their product selectivities were considerably different: linear hydrocarbons of C3-C9 were mainly produced on MWW, while the yield of C2= and aromatics were high on MFI. Polyaroamatic hydrocarbons (PAHs) were accumulated on MWW, but a small amount of benzene and aromatics on MFI. The impregnation of phosphorous on MWW caused significant decreases in the catalytic activity and toluene adsorption, but the decreases were relatively small on MFI. Although the straight pores of MWW were inactive in the MTO reaction due to the accumulation of PAHs, its circular pores which suppressed the formation of PAHs sustained catalytic activity for the production of linear hydrocarbons. Therefore, the impregnation of phosphorous on the circular pores of MWW caused a significant decrease in catalytic activity. The phosphorous impregnation on the cross sections of MFI altered the product selectivity due to the neutralization of strong acid sites, but catalytic deactivation was negligible. The difference of MWW and MFI zeolites in the MTO reaction was explained by their difference in pore structure.