Fuel additives are widely used as octane number improvers, oxygenates, emission depressors, and corrosion inhibitors to promote combustion processes of liquid fuel. In this work, six kinds of fuel additives, including ethanol, butanol, dimethyl carbonate, dibutyl carbonate, methyl tert-butyl ether, and tri-tert amyl glycerol ether, were studied by ReaxFF molecular dynamics simulations. The bond dissociation reactions were found to be more dominant at the early stage than oxidation reactions, which means the unimolecular reactions were the main pathways of primary reactions in hydrocarbon combustion. The rate constants of primary reactions of ethanol combustion were much smaller than those of other systems, which were in good agreement with the product distribution analysis and previous work. The main reaction pathway and relative rate constants for all systems were evaluated. Four kinds of main radicals, including center dot CH3, center dot center dot CH2, center dot OH, and center dot HO2, were detected, and the number variation with time are presented. The number of .OH radicals was the largest among those four radicals, and it was found to gradually increase with time except for ether systems; the number of center dot CH3 and center dot center dot CH2 radicals sharply increased first and then gradually decreased. Hopefully, the results obtained in this work will be helpful to future design and screening of new fuel additives.