Heavy oils contain many kinds of organic compounds which have complex structures. Thus, it is difficult to determine these characteristics to develop suitable catalysts. Recently, due to the development of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS), the detailed composition data of heavy oils can be obtained. In this research, the authors proposed a new method to analyse chemical reactions using the input/output composition data from FT-ICR-MS. In this method, representative chemical reactions were defined and assumed the series of reactions linearly. As a result, the conversion ratios of each chemical reaction can be simply obtained and statistically compared by molecular structures. The authors applied this method to a residue desulfurization in a petroleum refinery as a case study and compared the reaction ratios by molecular structures. From this analysis, the authors found that the molecular structure significantly affects the conversion ratio in desulfurization reaction and captured the characteristics of this reaction. Therefore, this analysis might be promising to analyse reactions for providing insights into catalysts and process design.