Due to the existence of an ester group, methyl butanoate (MB) has been a candidate for biodiesel surrogate, while methyl crotonate (MC) has been chosen to represent unsaturated species in biodiesel. In order to have a comprehensive understanding of the effect of ester molecular structure on its oxidation and formation of polycyclic aromatic hydrocarbons (PAHs) and soot, MB and MC have been chosen as test fuels in the present work. Experiments have been performed using an atmospheric laminar flow reactor and a coflow laminar diffusion flame burner. Species profiles during the oxidation process, soot volume fraction data, and transmission electron microscopy (TEM) images of soot have been obtained by using a flow reactor and coflow laminar diffusion flame burner. The reaction pathways of oxidation and PAH formation have been analyzed using a newly developed and validated kinetic model which contains 840 species and 12,851 reactions. MC has a much stronger ability in producing small-molecule unsaturated species that are commonly known as soot precursors and will finally lead to the formation of soot. As for PAH formation, simulation using SENKIN that covers a wide range of conditions has been performed, and a larger amount of PAHs can be observed in a wide range of temperature and equivalent ratios during MC oxidation when compared to MB. Soot volume fraction distribution in MB and MC coflow diffusion flames has been detected using 2D laser-induced incandescence technique, and TEM images of soot particles have also been acquired. The inception and growth of soot particles in MC flame are more obvious than those in MB. From the formation of small-molecule unsaturated species to soot particles, MC shows a stronger soot tendency than MB.