Lubricating oil is a high value-added petroleum product with a wide variety of application. It’s a challenging task to make full use of raw materials with various properties from different sources to produce the ideal lubricant products. Composition analysis at molecular level, instead of general analysis of physico-chemical properties, provides a deep view for processing optimization. In this study, comprehensive and in-depth analysis of molecular composition was established for characterization of lubricant products obtained by different processing conditions using ultra-high resolution mass spectrometry. Based on the molecular characterization of both feeds and products, the change of compound distribution was monitored during the conversion process, and the mechanisms of removal of nitrogen, oxygen and sulfur-containing compounds were summarized, which set a stage for process optimization.