A methodology of surrogate fuel formulation by directly using molecular structure and functional groups for both oxygenated and hydrocarbon fuels is proposed and investigated. The novelty of this method is to construct surrogate fuel mixtures by directly matching the molecular structure and the key functional groups instead of using the combustion property targets explicitly. This method is tested by using two different classes of fuels, biodiesel and jet fuel. For biodiesel, by using four functional groups such as CH3-, -CH2-, -CH2-CH=CH-, and -COO-CH3, a surrogate mixture of methyl-9-decenoate, 1,4-hexadiene and n-dodecane is formulated to demonstrate the efficacy of this method by comparing the resulting gas phase combustion targets between the formulated surrogate and biodiesel. For jet fuels, five functional groups such as CH3, CH2, CH, C, and phenyl were used to construct the Princeton 1st and 2nd generation surrogate jet fuel mixtures. The simulated results are compared with the experimental data and the results predicted by other surrogate fuel formulation methods. The comparisons show that the present method can formulate surrogated mixtures of both oxygenated and hydrocarbon real fuels and reproduce the combustion characteristics. Therefore, this method can be used not only for biodiesel and jet fuels, but also for other alternative fuels. (C) 2015 Elsevier Ltd. All rights reserved.