The aim of this study was to establish an ultra-performance liquid chromatography coupled with triple-quadrupole tandem mass spectrometry method with positive and negative ion exchange scanning mode for simultaneous quantification of two different skeleton components to reveal the differences among raw and processed Angelicae Pubescentis Radix. The results of methodology showed that each compound had good linearity and recovery rates. And the chemometrics results indicate that there were differences not only in Angelicae Pubescentis Radix samples from different sources but also in raw and processed Angelicae Pubescentis Radix. The results of this study confirm that the method has been successfully applied in simultaneous determination and discovering the difference of two different skeleton components between raw and processed Angelicae Pubescentis Radix for the first time. In short, the method could be an effective tool for detecting the quality of traditional Chinese medicine, and can better reveal the difference between raw and processed Chinese medicine from different sources.