Hierarchical zeolites were synthesized by alkali treatment and their applications in Fischer–Tropsch (FT) synthesis were studied. It was found that alkali treatment not only created hierarchical structure but also could tune cobalt-support interaction. The dissolution of Si by alkali treatment became easier with the increase of Si/Al ratio, and thus the amount of mesopority increased. An optimal Si/Al molar ratio was identified over the zeolite with Si/Al ratio of 80, which was found to be superior to other catalysts in terms of better diesel selectivity and lower CH4 selectivity due to its relatively narrow bimodal pore size distribution and moderate cobalt-support interaction. Meanwhile alkali treatment could enhance cobalt-support interaction via the formation of ɑ-SiO2, Co/MZ-120 catalyst showed the lowest FT activity and higher CH4 selectivity due to the increase of such new phase.