Fischer–Tropsch (F–T) fuel, synthesized from coal-to-liquid (CTL), is an alternative fuel with clean and efficient characteristics. In this study, a surrogate fuel model was developed, including n-dodecane (n-C12H26) and iso-octane (i-C8H18), which represents the n-alkane and iso-alkane in F–T fuel synthesized from CTL, respectively. The proportions of the components in the surrogate fuel are determined by the characteristics of the practical fuel, including cetane number (CN), C/H ration and component composition. For the establishment of the skeletal mechanism model, firstly, based on a two-step direct relationship graph (DRG) and the computational singular perturbation (CSP) importance index method, a reduced model of n-dodecane was developed involving 159 species and 399 reactions, while the detailed n-dodecane mechanism consists of 1279 species and 5056 reactions. Then, the n-dodecane skeletal mechanism was constructed based on a decoupling methodology, involving the skeletal C12 mechanism from the reduced mechanism, a C2-C3 sub mechanism and a detailed H2/CO/C1 sub mechanism. Finally, the skeletal mechanism for the F–T surrogate fuel was developed, including the n-dodecane skeletal mechanism and an iso-octane macromolecular skeletal mechanism. The final mechanism for the F–T diesel surrogate fuel consists of 169 species and 406 reactions. The n-dodecane skeletal mechanism and iso-octane skeletal mechanism were validated on various fundamental experiments, including the ignition delay in shock tubes, the primary species concentrations in jet-stirred reactors and the premixed laminar flame over wide operating conditions, which show great agreement between the predictions and measurements. Moreover, an F–T surrogate fuel mechanism was employed to simulate the combustion characteristics of an engine using computational fluid dynamics (CFD). The results show that the mechanism can predict the performance of F–T fuel combustion in engine accurately.