The invention discloses a preparation method of a cobalt-based Fischer-Tropsch synthesis catalyst. Silica gel is used as a carrier, and a two-time dipping method is used for loading an active component Co, wherein when the primary dipping process is carried out, the pH of a cobalt salt dipping solution is higher; and when the secondary dipping process is carried out, the pH of the cobalt salt dipping solution is lower. When the cobalt-based Fischer-Tropsch synthesis catalyst prepared by the method of the invention is applied to Fischer-Tropsch synthesis reaction, higher conversion rate and more than C5 product selectivity are kept, and simultaneously, the selectivity of carbon dioxide and methane is lower. The invention has ideal economical efficiency and is environment-friendly.