Biodiesel is a potential alternative fuel which can meet the growing need for sustainable energy. Partially premixed compression ignition (PPCI) is an important low-temperature combustion strategy to reduce NOx and soot emission of diesel engines. To investigate partial premixing impact on particle formation in flames of biodiesel or biodiesel surrogates, an experimental study was performed to compare the soot morphology and nanostructure evolution in laminar co-flow methyl decanoate non-premixed flame (NPF) and partially premixed flame (PPF). The thermophoretic sampling technique was used to capture particles along flame centerlines. Soot morphology information and volume fraction were obtained from TEM analysis and nanostructure features were evaluated by HR-TEM. With primary equivalence ratio of 19, gas temperature of PPF is higher along flame centerline compared with NPF. The results show an initially stronger sooting tendency in PPF at lower positions. Simulation work reveals that partially premixed oxygen promotes fuel decomposition and leads to higher acetylene yield, which is important for soot inception and growth. With rising height, the increase of soot volume fraction of the PPF is suppressed, while in NPF it increases rapidly and reaches the peak, because primary oxygen can enhance soot oxidation by increasing OH radicals in medial flame region. The molecular weight distributions of aromatic rafts were evaluated on the basis of fringe length distribution. The distribution is shifted to higher weight in PPF at the height of 40 and 50 mm. It is indicated that partial premixing promotes the growth of aromatic structure and increases the fringe length in the region where soot particle are deemed to be mature. In addition, the fringe tortuosity of PPF is obviously higher than that of NPF along the centerline of flames, which indicates that partially premixed oxygen in MD can promote the formation of species with odd number carbons and related PAHs.