Preasphaltene (PA) defined as tetrahydrofuran (THF) soluble and toluene insoluble is an important intermediate product of direct coal liquefaction (DCL). Investigating the structure of PA not only can improve the DCL technology but also can help us understand the structure of coal. In this paper, two types of PAs from the DCL residue of 6 t/d Shenhua process developing unit (PDU) and the products of a batch hydroliquefaction in an autoclave were first separated into different subfractions by the column chromatography. Then, the obtained subfractions were characterized by Fourier transform infrared spectroscopy (FTIR), ultraviolet–visible spectroscopy (UV) and fluorescence spectroscopy (FL), matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and gel permeation chromatography (GPC), respectively. The results indicate that the PA from DCL mainly exists in the form of aggregates. Two different PAs show similar distribution of subfractions, but the PA(B) obtained by the batch liquefaction displays larger molecular weight than the PA(A) from Shenhua PDU technology. A molecule of PA contains two or more aromatic nuclei (fluorophors). Subfractions I–III consist of smaller fused aromatic nucleus than the other subfractions. In general, their intermolecular aggregations increase from subfraction I to VII, and the aggregation of PA(A) subfractions is stronger than that of corresponding PA(B) subfractions.