Surfactant‐free microemulsions (SFMEs) cleaning technology can effectively separate and recover petroleum pollutants from oil‐based drilling cuttings (OBDCs). The identification of the molecular composition of OBDCs is helpful to accurately grasp the conversion mechanism of organic matter. Therefore, the understanding of the mechanism of petroleum removal at the microscopic molecular level in the cleaning process needs to be further studied. The conversion mechanism of organic matter during the use of SFMEs to clean OBDCs was investigated by positive ion atmospheric pressure photoionization Fourier transform ion cyclotron resonance mass spectrometry (+APPI FT‐ICR MS). The results show that the SFMEs cleaning technology can separate and recover CH and CHO organic matter in OBDCs, but there is still a small amount of organic matter with high molecular weight and unsaturated degree in OBDCs that has not been separated. The majority of this organic matter is CH, accounting for 91 %, and it is mainly polycyclic aromatic hydrocarbons. A total of 255 kinds of organic matter in 110# industrial white oil were detected in the recovered oil after treatment, accounting for more than 99 % of the total, which has a certain recoverable value. This study can provide a theoretical reference for the efficient degradation of OBDCs.