Extensive researches have been focused on the analysis of organic compounds in coals at the molecular level to reveal the characteristics of coals with different ranks and/or origins. Mass spectrometry, in association with a variety of sample inlet systems, has revolutionized the analysis of complex mixture like coals and should be the most rapidly developed analytical technology in the last 20 years. Various ion sources have been developed that dramatically increase the selectivity and sensitivity for mass spectrometry. Through various ionization techniques, the exact structures of coals can be obtained, which will explore the application of coal directional conversion and facilitate the utilization of coals cleanly and efficiently.