The thermochemical conversion of biomass energy contributes to the goals of carbon peaking and carbon neutrality. In this paper, the evolution of the chemical structure of corn stalk (CS) during hydrothermal carbonisation (HTC) was investigated and the effect of temperature on the physicochemical properties, carbon skeletal structure, and surface functional groups of the obtained hydrochar was explored. The results indicate that the H/C and O/C atomic ratios of the hydrochar decreased as the HTC temperature increased. The -C-(O, N), –C=O, and O–C=O bonds in the CS rapidly formed aromatic structures through cyclisation, condensation, or polymerisation, which in turn increased the -C-(C, H)/C=C content in the hydrochar. The oxygen-containing functional groups in the CS and hydrochar were mainly carbonyl (C=O), aromatic ring (C=C), ether oxygen bond (C–O), alcohol-phenol oxygen bond (C–OH), and carboxyl (O=C–O) groups. A high HTC temperature lowered the degree of substitution of the aromatic hydrocarbons and increased their degree of condensation. The hydrolysis stage and the formation of aromatic structures were competing processes. At low temperatures, the hydrolysis reaction was dominant and the generation of aromatic structures was secondary. However, at high temperatures, the intermediate compounds underwent transformation after hydrolysis, and the generation of aromatic structures was more competitive.