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Abstract Background Chrysanthemi Flos is a traditional Chinese medicine with a long history of medicinal use. Prior research suggests that the intrinsic composition of Chrysanthemi Flos is affected by shade-drying and oven-drying methods. Nevertheless, the effects of these methods on the proteins and metabolites of Chrysanthemi Flos have not been extensively studied. Methods The TMT (tandem mass tag) quantitative proteomics method and the LC–MS/MS (liquid chromatography-tandem mass spectrometry) non-targeted metabolomics method were used to systematically study the differences in the proteins and metabolites during the process of drying Chrysanthemi Flos in the shade and an oven. Results Differentially accumulated metabolites and abundant proteins were primarily enriched in the purine metabolism, pyrimidine metabolism, cyanogenic amino acid metabolism, phenylpropanoid biosynthesis, and starch and sucrose metabolism pathways. Primary metabolites, such as guanine, xanthine, cytidine 5'-diphosphate serine, L-isoleucine, stearidonic acid, alginate, and inulin, play a crucial role in providing energy for Chrysanthemi Flos to withstand desiccation stress. The upregulation of ferulate-5- hydroxylase (F5H), shikimate O hydroxycinnamoyltransferase (HCT), caffeoyl-CoA O-methyltransferase (CCoAOMT), and chalcone isomerase (CHI) enzymes promotes the synthesis of flavonoids, including sinapic acid, caffeoyl shikimic acid, and naringenin chalcone, which possess antioxidant properties. Despite the notable improvements in energy metabolism and antioxidant capacity, these enhancements proved insufficient in halting the senescence and ultimate demise of Chrysanthemi Flos. Moreover, the shade-drying method can inhibit protein expression and promote the accumulation of bioactive components, but the drying efficiency is low, while the oven-drying method exhibits rapid drying efficiency, it does not effectively preserve the components. Conclusion Our study offers a comprehensive explanation for the changes in protein expression and metabolite conversion observed in shade-dried and oven-dried Chrysanthemi Flos, also providing a foundation for optimizing the drying process of Chrysanthemi Flos.