The influence of different iron carbides on the activity and selectivity of iron-based Fischer–Tropsch catalysts has been studied. Different iron carbide phases are obtained by the pretreatment of a binary Fe/SiO2 model catalyst (prepared by coprecipitation method) to different gas atmospheres (syngas, CO, or H2). The phase structures, compositions, and particle sizes of the catalysts are characterized systematically by XRD, XAFS, MES, and TEM. It is found that in the syngas-treated catalyst only χ-Fe5C2 carbide is formed. In the CO-treated catalyst, Fe7C3 and χ-Fe5C2 with a bimodal particle size distribution are formed, while the H2-treated catalyst exhibits the bimodal size distributed ε-Fe2C and χ-Fe5C2 after a Fischer–Tropsch synthesis (FTS) reaction. The intrinsic FTS activity is calculated and assigned to each corresponding iron carbide based on the phase composition and the particle size. It is identified that Fe7C3 has the highest intrinsic activity (TOF = 4.59 × 10–2 s–1) among the three candidate carbides (ε-Fe2C, Fe7C3, and χ-Fe5C2) in typical medium-temperature Fischer–Tropsch (MTFT) conditions (260–300 °C, 2–3 MPa, and H2/CO = 2). Moreover, FTS over ε-Fe2C leads to the lowest methane selectivity.