The effect of mesoporous structure of ZSM-5 on the properties of cobalt-based catalysts for Fischer-Tropsch synthesis was studied in this work. ZSM-5 and amorphous SiO2 supports have also been applied for comparison. It was shown that post treatment of ZSM-5 catalyst by NaOH solution improved the catalytic performance to produce higher amount of liquid hydrocarbons. The hierarchical structure combining with the acidity of meso-ZSM-5 had great effect on increasing the selectivity to C5-18 hydrocarbons and preventing the formation of CH4. The more acid sites of the support promoted catalytic cracking reaction of olefinic hydrocarbons to light hydrocarbons, the lower olefin to paraffin ratio was observed over Co/meso-ZSM-5 catalyst compared with that of Co/SiO2 catalyst.