Abstract: Fischer Tropsch synthesis is an important approach to convert carbon source, such as coal, natural gas, biomass and so on, into synthetic fuels and value- added chemicals, i.e. lower olefins, gasoline, jet fuel, diesel and wax. Recently, Fischer Tropsch synthesis recapture our attention under the international carbon neutrality context as an important carbon utilization route with high carbon utilization efficiency. Fe, Co, Ru are the main active metal for Fischer Tropsch synthesis. Among which cobalt based Fischer Tropsch synthesis catalysts have gained the interests both in industrial and academic area owing to the high stability, resistance to oxidation, low reverse water gas shift (RWGS) activity, high unbranched long-chain hydrocarbons selectivity and also the acceptable expense. To improve the mass specific activity and elucidate the origin for the catalytic activity, researcher have employed multiple techniques to explore the microstructure and construct the structure-activity relationship. Besides, considering that the chain growth via C−C coupling following the CH2 polymerization mechanism, the products selectivity is limited by the Anderson–Schulz–Flory (ASF) distribution with the theoretical value for C5-C11 (gasoline), C8-C16 (jet fuel) and C10-C20 (diesel) is 48%, 41% and 40%, respectively. Thus the regulation for products distribution for the selective formation of targeted product is one of the biggest challenges in Fischer Tropsch synthesis. This review summarized the recent progress for several key influencing factors in cobalt based Fischer Tropsch synthesis, i.e. particle size, crystal phase, support, promoter and special spatial structure. Besides, the prospects for the future research directions were given. The controllable synthesis of a catalytic system that coupled with a cobalt-based catalyst and a zeolite or a cobalt confined catalytic system to highly selectively control the products distribution is a future development direction. Moreover, issues arising from the scale-up of these catalytic systems in the industrial application, such as mass transfer and heat transfer, deserve special attention. In addition, due to the fact that metallic cobalt is easily oxidized in the air, the results characterized under ex-situ conditions may deviate from the real situation. Employing a variety of in-situ techniques to detect the true structure of cobalt-based catalysts under working conditions as well as observe the dynamic evolution process under the reaction atmosphere to establish the structure-activity relationship between the real microstructure of the working catalysts and the catalytic performance, which will help to deeply understand the origin of the activity of the Fischer-Tropsch reaction.