Fe/SiO2 catalysts with different Fe/Si molar ratios were used to investigate the effects of silica on chemical/structural properties and Fischer–Tropsch synthesis (FTS) performance of iron-based catalysts. In the chemical aspect, silica interacts with Fe species by the formation of Fesingle bondOsingle bondSi structure, which further transforms into an Fe2SiO4 phase during FTS reaction. The interaction largely disturbs the electronic structure of Fe atoms in iron oxide phases and in turn resists the reduction and activation of catalysts. In the structural aspect, silica increases the dispersion of Fe species and inhibits the aggregation of active iron particles. Addition of silica largely changes the adsorption sites of catalysts, i.e., decreases the number of weak H adsorption sites but improves the adsorption strengths of H, C, and O on reduced or carburized catalysts. With increasing amounts of silica, the chemical and structural effects cause the firstly decrease and then the increase of the initial FTS activity and the selectivities of heavy hydrocarbons and olefins during the Fischer–Tropsch synthesis. In addition, an important finding is that a proper amount of silica apparently suppresses the methane selectivity and stabilizes the iron carbide in the FTS reaction.