A matrix assisted laser desorption/ionization time of flight mass spectrometric(MALDI-TOF MS) method with N alkylpyridinium isotope quaternization(NAPIQ) was developed for the rapid identification of microbial contamination in herbs in this paper.The sterols in herbs were extracted with chloroform,and then derivatized with three reagents,ie.pyridine,D5 pyridine and trifluoromethanesulfonic anhydride.The derivatization could significantly enhance the ionization of sterols in the analysis by MALDI-TOF MS.Only phytosterols such as sitosterols and stigmasterols in the fresh traditional Chinese medicine were detected by this method,while the zoosterols and the mycosterol such as lanosterol and ergosterol were observed in the mass spectra of moldy herbs.Furthermore,the method was compared with the microbial enumeration method in Chinese Pharmacopoeia(2015 edition).No molds in the fresh herbs were detected by the microbial enumeration method,while the microbial counts in the moldy herbs significantly exceeded the threshold of 102 cfu/g.Results showed that the MALDI-TOF MS combined with NAPIQ provided an alternative method for the identification of potential moldy herbs.