Co/NGA catalysts were one-step hydrothermal synthesized during the construction of three-dimensional nitrogen-doped graphene aerogel (NGA). The structure and properties of the catalysts were characterized by TGA, Raman, FTIR, XRD,TEM, SEM, XPS and H-2-TPR, and their catalytic performance was tested by Fischer-Tropsch synthesis (FTS) reaction. Characterization and reaction results showed that higher cobalt dispersion was found on the catalyst with higher cobalt loading, and majority of cobalt species in the freeze-dried samples was fcc phase Co degrees. Excessive cross linking originated by high Co2+ concentration during the construction of 3D NGA led to the restraint of mass transfer of reactants to cobalt active sites, and therefore, lower FTS activity was observed on the catalysts with higher cobalt loadings. The fcc phase Co degrees in fresh Co/NGA catalysts was transformed in to hcp phase Co degrees during FTS reaction, and as a result, catalytic activity was increased with increasing time on stream.