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Graphical abstract An economic and green "couplet medicine" strategy was proposed for the first time for preventing Chinese medicinal materials from toxigenic fungi and aflatoxins contamination. Highlights • Toxigenic fungi and aflatoxins contamination affect the quality and safety of Chinese Medicinal Materials. • An economic and environment-friendly "couplet medicine" strategy prevents Chinese Medicinal Materials from the contamination. • The green strategy with low cost and little labor is preferred for scientific preservation of Chinese Medicinal Materials. • Embedding and stacking methods for practical operation to prevent Chinese Medicinal Materials away from toxigenic fungi. Abstract An economic, safe and environment-friendly strategy for preventing Chinese medicinal materials from fungi and aflatoxins contamination is in great need. This study aimed to develop a "couplet medicine" technique with low cost, little time and few labors for the first time for scientific preservation of Radix Notoginseng by investigating the inhibitory efficacy of some aromatic Chinese medicinal materials regarding their anti- Aspergillus flavus properties with the mold changes and aflatoxins accumulation as the detection indexes. An ultra-performance liquid chromatography with fluorescence detection method was validated for sensitive determination of four aflatoxins in Radix Notoginseng without or with the effects of protector from the couplet medicines. It was found that Cortex Cinnamomi , Fructus Anisi Stellati , Flos Caryophylli and Cortex Moutan with strong anti- A. flavus activities could be the potential protector medicines to prevent Radix Notoginseng from molds and aflatoxins contamination. After co-storage of one of the four candidates with Radix Notoginseng to form "couplet medicine", expected results expressed that Cortex Moutan was the best protector medicine at the weight ratio of protector (Cortex Moutan): protégé (Radix Notoginseng) of at least 2:1 (w/w). In practice, the "couplet medicine" of Cortex Moutan - Radix Notoginseng designed through the embedding and stratified stacking modes could effectively prevent toxigenic fungi contamination and aflatoxins residue in Radix Notoginseng to warrant the quality and safety of this highly-valuable Chinese medicinal material. The green "couplet medicine" strategy with lower cost and less labor can be preferred for scientific preservation of Chinese medicinal materials, foods and other matrices. [ABSTRACT FROM AUTHOR]