Abstract To develop effective catalysts for α-pinene isomerization reaction is important to get high valuable products. A hierarchical mordenite molecular sieve is prepared using alkaline treatment assisted by the microwave radiation. After the alkaline treatment, the relative crystalline decreases by ~20% and mesopores are introduced in the mordenite molecular sieve. Compared to conventional heating method, microwave assisted alkaline treatment exhibits a selective etching of zeolitic silicon atoms. Aluminum atoms adjacent to silicon atoms are extracted to form Al–OH hydroxyl groups. These extracted aluminum atoms are reconnected to zeolitic silicon atoms. Mordenite after microwave assisted alkaline treatment has a good dispersion of mesopores, higher retention of BrOnsted acid sites in 12-membered rings, and lower concentration of Lewis acid sites. The isomerization reaction of α-pinene suggests that alkaline treatment increases the accessibility of acid sites for α-pinene molecules. The hierarchical porosity increases the conversion of α-pinene from 46.1 to 94.7%. The yields for camphene and limonene increase by 17.0 and 5.4%, respectively. Disproportionation of limonene is inhibited when using microwave assisted alkaline treated mordenite due to a low concentration of Lewis acid sites. These results are important to propose a facile post modification method to realize a selective extraction of zeolitic framework atoms.