Large uncertainty among the measured uptake coefficients of O(3) on soot highlights the importance of the sources and chemical structures of soot samples in this reaction. Soot samples with different microstructures were prepared by combusting n-hexane under controlled conditions. Their reactivities to O(3) were further investigated using in situ Raman spectroscopy. The fuel/oxygen ratio in the combustion experiments not only affected the diameter of the primary particles, but also influenced the micro-chemical structure of soot. Average diameters of soot particles decreased with the decreasing fuel/oxygen ratio. Compared to the "fuel-rich" flame soot, the "fuel-lean" flame soot showed lower structural uniformity with higher disordered carbon content at the graphene layer edges (D1 band) and the surface graphene layers (D2 band) and the amorphous carbon content (D3 band). This disordered carbon was identified as the reactive component for the ozonization of both the "fuel-rich" and "fuel-lean" flame soot samples. The kinetics study demonstrated that the disordered carbon at the surface graphene layers was more active than that at the graphene layer edges in one sample, and the reactivity of these two microstructures types to O(3) in the "fuel-rich" flame soot was higher than that in the "fuel-lean" flame soot.