Solvent extraction is an effective approach to analyze the molecular features of coal and to reveal the transformation mechanism of heteroatoms. In order to accurately figure out the transformation and distribution of heteroatoms during extraction, Naomaohu coal (NMHc), Hypercoal (HPC), and Extraction residue (ER) were systematically analyzed with Fourier transform infrared (FTIR) and X-ray photoelectron spectrometer (XPS). The liquid extract was characterized using Atomic Emission Detector for Gas Chromatography (GC-AED) and gas chromatograph with mass spectrometer (GC–MS). In addition, the distribution characteristics of gas products were examined by gas chromatograph (GC). The results suggest that the solvents with high polarity, strong hydrogen donating capacity, and similar solubility to coal could promote the separation of organic compounds from coal. The extraction yield of xylene with coal increased with increasing temperature. Based on the “Similarity-Intermiscibility” principle, the extracts of xylene were mostly aromatic hydrocarbons and alkanes. The heteroatom-containing species were difficult to be extracted by xylene. Sulfur and oxygen were easily transformed into gas products such as H2S, SO2, CO, and CO2. Moreover, nitrogen compounds were hard to be extracted and recombined. Most of the compounds containing O, S, Cl, and other inorganic substances can be almost completely transferred into the residue through the extraction process. After the thermal solvent extraction, the heteroatoms were primarily present as organic matter in the ER and extract, such as thiophene, pyrrole, pyridine, ketone,and their homologues. The molecular structure of coal was reorganized to be of high thermal and chemical stability, especially for the heteroatom-containing species.