Dendrobium chrysotoxum stems (DCS) are valuable in the traditional Chinese medicine and in functional foods catagory. Their bioactive composition is critically influenced by the post-harvest drying methods. Here, we evaluated the effect of five drying methods (shade drying (SD), oven drying (OD), vacuum freeze-drying (FD), microwave drying (MD), and infrared drying (ID)), on the bioactivity of the compounds in the DCS. OD-treated stems exhibited elevated total flavonoid contents (TFC) and total phenolic content, along with strong antioxidant activities. Although ID and MD yielded higher polysaccharides and alkaloids contents, they caused a marked deterioration in appearance. In contrast, FD better preserved the stem color and yielded higher erianin contents and anti-inflammatory activities than the thermal drying methods. Under OD, zeatin biosynthesis was specifically differentially regulated, as compared to the other methods. Additionally, L -homoserine, (7 S , 8 S )-DiHODE, and L -pipecolate showed positive correlations with erianin and TFC in the OD group. Based on a comprehensive evaluation, this study offers scientific and technical support for selecting appropriate drying methods to achieve desirable appearance and product quality of DCS.