A new process, in situ deposition method, was developed to unveil Fe phase evolution behavior in iron-based Fischer-Tropsch synthesis (FTS). In detail, Fe(CO)x-containing syngas (CO/H-2) was fed into a fixed-bed reactor where Fe(CO)x directly decomposes to metallic Fe with subsequent favorable carburization to form active chi-Fe5C2 on SiO2 under FTS reaction conditions. This facile process gives a high chi-Fe5C2 content (80-90%) without Fe3O4 phase in spent catalyst. In contrast, the 5.3Fe/SiO2 prepared by the conventional impregnation method results in very low chi-Fe5C2 content (14.5%) and high Fe3O4 content (47%) in spent catalyst, which is ascribed to the strong Fe oxide-SiO2 interaction hindering its deep reduction into metallic Fe but terminating as FeO. The reduced FeO could not be efficiently carburized into chi-Fe5C2 and tends to oxidize into Fe3O4 during the FTS reaction. Furthermore, the factors determining CO2 selectivity are systematically investigated based on abundant experiments. Results show that CO2 selectivity is closely related to CO conversion, Fe phase composition, reaction conditions, and the presence of K promoter. In brief, when the factor enhances H-star/C-star ratio on chi-Fe5C2, the reaction of dissociative O-star from CO shifts towards hydrogenation to H2O despite that its reaction with CO star to form CO2 via Boudouard mechanism is kinetically favorable. In addition, CO2 selectivity could be reduced via reverse water-gas shift (RWGS) reaction on Fe3O4 with H2O generation.