A series samples with different types of acid sites: Bronsted acid sites, Lewis acide sites, and extra-framework aluminum (EFAL) species were investigated in selective catalytic reduction of NOx with methanol (methanol-SCR). Comparing with Bronsted acid sites (BAS) and Lewis acid sites (LAS) present in zeolites, EFAL species exhibit much higher catalytic activity. EFAL species were confirmed in calcined HZSM-5 by FT-IR with pyridine and in-situ DRIFT. Reaction intermediates were investigated by in-situ DRIFT measurements, and the reaction mechanism was proposed. Formamide and methyl nitrite species was the key intermediates of methanol-SCR reaction and formamide further react with nitrous compounds to produce nitrogen and nitride oxide. EFAL species promoted the adsorption of methyl nitrite and nitromethane species and the formation of formamide.