This work concerns the oxidation of biodiesel surrogates in a CI engine. An experimental study has been carried out in a single-cylinder common-rail CI engine with soybean biodiesel and two biodiesel surrogates containing neat methyl decanoate and methyl decanoate/n-heptane blends. Tests have been conducted with various intake oxygen concentrations ranging from 21% to approximately 9% at intake temperatures of 25°C and 50°C. The results showed that the ignition delay and smoke emissions of neat methyl decanoate were closer to that of soybean biodiesel as compared with methyl decanoate/n-heptane blends. A reduced chemical kinetic mechanism for the oxidation of methyl decanoate has been developed and applied to model internal combustion engines. A KIVA code, coupled with the Chemkin chemistry solver, was used as the computational platforms. The effects of various intake oxygen concentrations on the in-cylinder emissions of OH and soot were discussed. Based on the analysis of the concentration distribution of OH emissions, the impact of the intake oxygen concentration on the ignition delay was pointed out. As the intake oxygen concentration decreased from 21% to 12.4%, the soot emission increased. However, with the intake oxygen concentration of 10.4%, the soot emission was lower than the peak value.