The existence of heteroatomic compounds with complex structure and different polarity in the asphaltene of medium and low temperature coal tar (M/LTCT) limits its processing and utilization. Combined with negative ion electrospray ionization source (ESI), Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) was used to characterize the molecular composition of O, N, and S heteroatom compounds in M/LTCT asphaltenes. Acidic oxygen-containing compounds (OCCs) and non-basic nitrogen-containing compounds (NCCs) in asphaltenes were identified, except for sulfur-containing compounds (SCCs). The mass spectra showed that the heteroatom compounds in asphaltene mainly existed as NX, N1OX, N2OX, N3OX, N4OX, N5OX, N6OX, and OX class species (where x = 1–6). The M/LTCT asphaltenes were enriched with O4, N4, and N1O1 class species. The core structure of O4 class species were likely to be composed of 1–7 aromatic rings with 4 phenolic hydroxyl groups, the core structure of N4 class species were likely to be comprised of 4–7 aromatic rings with a piperazine ring and a pyrazole ring, and the core structure of N1O1 was mainly 3–6 aromatic rings with a phenolic hydroxyl group and a pyrrole ring. These results suggest that more condensed NCCs and OCCs with short, substituted alky side chains are presented, which are more easily to undergo condensation to generate fused molecules, making it too difficult to be removed by hydrogenation. Through the analysis of the molecular structures of OCCs and non-basic NCCs in M/LTCT asphaltenes, important information about the molecular composition can be obtained, which can provide basic data for the hydrogenation of deasphaltene.