Three-dimensionally ordered nanoporous structures were generated in carbon materials doped with metals and nitrogen as catalytically active sites for electrochemical reactions. Free-base and metal phthalocyanines with a strategically designed molecular structure were used as carbon sources to obtain an ordered porous structure via homogeneous self-assembly with Fe3O4 nanoparticles as the pore template and the prevention of melting away during carbonization. The doping of Fe and nitrogen was achieved by a reaction between the free-base phthalocyanine and Fe3O4 through carbonization at 550 °C, while Co and Ni were doped using the corresponding metal phthalocyanines. The preference of these three types of ordered porous carbon materials for catalytic reactions was distinctly determined by the doped metals. Fe-N-doped carbon showed the highest activity for O2 reduction. Additional heat treatment at 800 °C enhanced this activity. CO2 reduction and H2 evolution were preferred by the Ni- and Co-N-doped carbon materials, respectively. A change in the template particle size was capable of controlling the pore size to enhance mass transfer and improve performance. The technique presented in this study enabled systematic metal doping and pore size control in the ordered porous structures of carbonaceous catalysts.