IntroductionMagnoliae officinalis cortex (MOC) has been used for thousands of years as a traditional Chinese herb. In Chinese Pharmacopoeia (2020 edition), it has two types of decoction pieces, raw Magnoliae officinalis cortex (RMOC) and ginger juice processed Magnoliae officinalis cortex (GMOC). The quality difference between RMOC and GMOC has not been explored systemically.ObjectiveThis study aimed to discover the quality difference between RMOC and GMOC, and clarify the effect of ginger juice during processing comprehensively.MethodsUltra‐performance liquid chromatography coupled with quadrupole time‐of‐flight tandem mass spectrometry (UPLC‐Q‐TOF‐MS/MS) and gas chromatography–mass spectrometry (GC–MS) were applied to study the non‐volatile and volatile components of RMOC and GMOC; electronic eye was applied for color measurement. Meanwhile, water processed Magnoliae officinalis cortex (WMOC) was studied as the blank sample.ResultsThere were 155 non‐volatile and 72 volatile substances identified. Between RMOC and GMOC, 29 distinctive non‐volatile and 34 distinctive volatile compounds were detected, among which 23 new compounds appeared and five compounds disappeared due to the addition of ginger juice during processing. The intensities of 12 common non‐volatile compounds and the relative percentage contents of four common volatile compounds showed significant differences between RMOC and GMOC. In color measurement of RMOC, GMOC, and WMOC, 14 common compounds with significant differences were discovered related to their color values, and their mathematical prediction functions were built.ConclusionThere were significant differences between RMOC and GMOC; the processing mechanism of GMOC would be carried out based on the differential compounds in further investigation.