In order to investigate the effects of methyl ester moiety on polycyclic aromatic hydrocarbons (PAHs) and NO x formation in biodiesel combustion, the combined models were developed based on detailed methyl butanoate (MB) oxidation model and n-butane model. Also, PAHs detailed reaction mechanism and NO x formation mechanism were added to the detailed models to form the combined models. The combined models were used to compare the combustion of n-butane and MB in a shock tube simulation to understand the effects of methyl ester moiety. The results indicated that compared with n-butane, the methyl ester moiety in MB leads to different reaction pathways, more CO and CO 2 formation and less formation of PAHs precursors such as ethylene and acetylene. In addition, a better chemical insight into the effects of methyl ester moiety on NO x formation was given, which will help to understand the combustion process of biodiesel.