Although dicofol has been widely banned all over the world as a kind of organochlorine contaminant, it still exists in the environment. This study developed a high-performance liquid chromatography coupled with mass spectrometry (HPLC-MS/MS) detection technique for dicofol, an environmental pollutant, for the first time using in-source fragmentation. The results confirmed thatm/z251 was the only precursor ion of dicofol after in-source fragmentation, andm/z139 andm/z111 were reasonable product ions. The main factors triggering the in-source fragmentation were the H+content and solution conductivity when dicofol entered the mass spectrometer. Density functional theory can be used to analyze and interpret the mechanism of dicofol fragmentation reaction in ESI source. Dicofol reduced the molecular energy from 8.8 ± 0.05 kcal/mol to 1.0 ± 0.05 kcal/mol, indicating that the internal energy release from high to low was the key driving force of in-source fragmentation. A method based on HPLC-MS/MS was developed to analyze dicofol residues in environmental water. The LOQ was 0.1 μg/L, which was better than the previous GC or GC-MS methods. This study not only proposed an HPLC-MS/MS analysis method for dicofol for the first time but also explained the in-source fragmentation mechanism of compounds in ESI source, which has positive significance for the study of compounds with unconventional mass spectrometry behavior in the field of organic pollutant analysis and metabonomics.