Methoxsalen (C₁₂H₈O₄) belongs to the class of furanocoumarins, and has been associated with various undesirable side effects, such as nausea, headache, and dizziness. It is used to treat psoriasis, vitiligo, as well as eczema. This compound can be commonly found in traditional Chinese medicines like Angelicae dahuricae and Angelicae pubescens. A reliable method for the identification and quantification of methoxsalen and its structural isomers is therefore necessary, and described using liquid chromatography-tandem mass spectrometry with multi-reaction monitoring (MRM) mode. The analysis time of the developed method has been reduced by three times from one reported method, with the use of a core-shell liquid chromatography column. Methoxsalen, bergapten and two unknown isomers have been separated by this method. Method validation data is presented and good precision and recoveries were obtained. The speed, selectivity and sensitivity of this method provides for high throughput, as well as utility for surveillance institutions.