Biodiesel is a potential alternative fuel which can meet the growing need for sustainable energy. Soot formation from biodiesel combustion is affected by many factors, such as combustion conditions and fuel components. To investigate partial premixing impact on particle formation in typical biodiesel surrogate flames, 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. Rapid thermocouple insertion technique was applied to obtain the temperature profiles. With primary equivalence ratio of 19, gas temperature of PPF was slightly higher along flame centerline compared with NPF. The results show an initially stronger sooting tendency in PPF at lower positions. Simulation works reveal that partially premixed oxygen promotes fuel decomposition and lead 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. It is illustrated that 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. In higher regions of the flame, the mean molecular weight of PPF is obviously higher than that of NPF, corresponding to the difference of soot volume fraction. It can be suggested that partial premixing can promote the aromatic growth and enhance the soot formation in higher regions. In conclusion, partially premixing effects on soot production is related to combustion condition and stage. Appropriate control strategies should be chosen to reduce the particle emission.