<h4>Aims</h4>In Sheng Nong's herbal classic in China, Rhizoma coptidis<sup>a</sup>(RC) could be used to treat Atopic dermatits<sup>b</sup>(AD), but its core ingredient(s) and mechanism remains unknown. The present study aimed to find out the ingredients against AD and expound its mechanisms.<h4>Materials and methods</h4>Seven alkaloids were isolated from RC to compare the inhibition against HaCaT cells by MTT assays and apoptosis of cells stimulated with TNF-α/IFN-γ by flow cytometry. The effects of target alkaloids against AD were evaluated on DNCB<sup>c</sup> (2,4-dinitrochlorobenzene)-induced atopic dermatitis in mice.<h4>Key findings</h4>Seven alkaloids were isolated from RC successfully. The results from MTT and flow cytometry indicated that among these alkaloids, only magnoflorine <sup>d</sup>(MAG) had no obvious toxicity on cells, but could inhibit the apoptosis of the cells stimulated with TNF-α/IFN-γ. Further animal experiments confirmed that MAG significantly attenuated the AD-like symptom and inhibited the AD-induced increases in IgE/IL-4, as compared with control (P < 0.01). Moreover, MAG reduced the low Δψ<sub>m</sub><sup>e</sup>(mitochondrial membrane potential) in HaCaT cells. The results of western blotting proved that MAG inhibited apoptosis of keratinocytes through decreasing the expressions of CTSB<sup>f</sup> (cathepsin B), Cyte C<sup>g</sup> (cytochrome C), Bid and caspase-3/7/8/9.<h4>Significance</h4>Overall, MAG inhibited apoptosis by decreasing the expression of apoptotic pathway-related proteins, and laid a foundation for the study of AD mechanisms.