For emulation of the chemical kinetic combustion phenomena and physical properties of S-8 POSF 4734 and Jet A POSF 4658, two surrogate fuels were formulated by directly matching their molecular structure and functional groups. The same functional groups, CH3, CH2, CH, C, and phenyl, were chosen to formulate the S-8 and Jet-A surrogates with n-dodecane/2,5-dimethiylhexane (0.581/0.419 mole fraction) and n-dodecane/2,5-dimethylhexane/toluene (0.509/0.219/0.272 mole fraction), respectively. The numerical results using the surrogate fuels were compared with the experimental data and the results predicted by other surrogate fuel formulation methods. The results show that the present method can formulate surrogate mixtures of both jet fuels and Fischer-Tropsch real fuels and reproduce the combustion characteristics in homogeneous ignition and the flow reactor oxidation process. The idea presented here could be extended to other real fuels with the appropriate choice of surrogate fuel components.