To investigate the effect of coordination features of Co(II)-glycine complex on the performance of Co/SiO2 for Fischer–Tropsch (FT) synthesis, Co(II)-glycine complex precursors were prepared by the conventional method, i.e., simply adding glycine to the solution of Co nitrate and novel route, i.e., reaction of glycine with cobalt hydroxide. The SiO2-supported Co catalysts were prepared by using the different Co(II)-glycine complexes. It is found that glycine is an effective chelating agent for improving the dispersion of Co and the mass-specific activity in FT synthesis when the molar ratio of glycine/Co2+ = 3, which is independent to the preparation method in this study. Significantly, the surface Co properties were significantly influenced by the coordination features of the Co2+ and the molar ratio of glycine to Co2+ in the Co(II)-glycine complex. Specifically, the Co(3gly)/SiO2 catalyst prepared by the novel route exhibits smaller and homogenous Co nanoparticles, which result in improved stability compared to Co-3gly/SiO2 prepared by the conventional method. Thus, the newly developed method is more controllable and promising for the synthesis of Co-based catalysts for FT synthesis.