Oxidant stimulation using Sodium Hypochlorite (NaClO) is proposed for enhancing coal seam permeability. To understand the effect of NaClO on different coal types, a subbituminous coal (Coal S) and a bituminous coal (Coal B) collected from the Surat Basin and Bowen Basin, Australia, respectively, were studied. The molecular structures of the two coals and their oxidised residues (Coal So and Coal Bo) were examined using Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy (ATR-FTIR), X-ray Photoelectron Spectroscopy (XPS) and solid state C-13 Nuclear Magnetic Resonance Spectroscopy (C-13 NMR). Based on the results, the molecular structure schematic models of the samples were established. Results illustrate that Coal S is less aromatic with longer aliphatic chains and more oxygen content, while Coal B has larger average aromatic clusters, as expected given its higher rank. NaClO prefers to oxidise aliphatic chains, particularly those with oxygen functional groups. NaClO tends to oxidise small aromatic rings first, evidenced by the loss of smaller clusters in coal S, leaving the larger aromatic clusters. NaClO then attacks the larger aromatic clusters, confirmed by the average cluster size decrease for Coal B. The oxidised Coal B (Coal Bo) has a similar molecular structure to raw Coal S. After oxidation, both coal residues exhibit lower aromaticity, longer aliphatic chains and more oxygen content. The decreased aromaticity suggests reaction between NaClO and benzene rings. The breakage of aromatic rings is further suggested to give rise to longer aliphatic chains. NaClO oxidation products enriches the coals in C=O and O-C=O for both coals. These findings observed fill a gap in knowledge on coal oxidation by NaClO and contribute to the decision of selecting the most suitable oxidant stimulation targets for enhancing coal permeability.