The evolution of surface functional groups (SFGs) and the graphitization degree of soot generated in premixed methane flames are studied and the correlation between them is discussed. Test soot samples were obtained from an optimized thermophoretic sampling system and probe sampling system. The SFGs of soot were determined by Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy after removing the soluble impurities from the soot samples, while the graphitization degree of soot was characterized by Raman spectrum and electron energy loss spectroscopy. The results reveal that the concentration of aliphatic C–H groups and C=O groups shows an initial increase and then decrease in the sooting history. The large amount of aliphatic C–H groups and small amount of aromatic C–H groups in the early stage of the soot mass growth process indicate that aliphatic C–H groups make a major contribution to the early stage of soot mass growth. The highest graphitization degree of soot appears at low height above the flame when the graphite core is formed. The graphitization degree rapidly decreases in the early mass growth stage then slightly increases in the maturation process. The results from transmission electron microscopy, SFGs, and the graphitization degree verify the assumption that the nascent soot consists of a graphite-like core and an aliphatic shell. There is a strong correlation between SFGs and graphitization degree in the early stage of the soot mass growth process. During the processes of coalescence and agglomeration, the correlation weakens. The SFGs may be related to the aggregate soot particle properties, such as fractal dimension.