In order to convert low temperature coal tar (LCT) into clean transportation fuels by hydrotreating (HDT), the changes of asphaltenes properties during HDT of LCT should be paid more attention. The HDT experiments were carried out in a trickle-bed reactor unit under various reaction temperatures, and asphaltenes were extracted from the liquid products. The properties and structure of asphaltenes were performed by X-ray diffraction, elemental analysis, size-exclusion chromatography, X-ray photoelectron spectroscopy, and nuclear magnetic resonance. Structural units analysis of average molecules and the variation trend of change in the structural parameters were revealed. The results showed that, with the temperature increase, the diameter of the aromatic sheet (La), interaromatic layer distance (dm), total carbon number (CT), and average alkyl chain length (n) decrease, while the aromaticity factor (fA) and aromatic carbon number (CA) increase. Moreover, the mechanism of HDT was studied to make the molecular structure of asphaltenes easier to understand. At the same time, the larger condensation degree of the asphaltenes molecules, the larger aromatic degrees, the removal of the alkyl side chain was more significant.