BackgroundDendrobium nobileandDendrobium chrysotoxumare important species of the genusDendrobiumand have great economic and medicinal value. However, the medicinal properties of these two plants remain poorly understood. This study aimed to investigate the medical properties ofD. nobileandD. chrysotoxumby conducting a comprehensive chemical profiling of the two plants. Additionally, active compounds and predictive targets for anti-hepatoma activity inD. chrysotoxumextracts were identified using Network Pharmacology.ResultsChemical profiling showed that altogether 65 phytochemicals were identified fromD. nobileandD. chrysotoxum, with major classes as alkaloids, terpenoids, flavonoids, bibenzyls and phenanthrenes. About 18 compounds were identified as the important differential metabolites inD. nobileandD. chrysotoxum. Furtherly, CCK-8 results showed that the extracts of stems and leaves ofD. nobileandD. chrysotoxumcould inhibit the growth of Huh-7 cells, and the anti-hepatoma activity of extracts were dose-dependent. Among the extracts, the extract ofD. chrysotoxumshowed significant anti-hepatoma activity. In order to find the potential mechanism of anti-hepatoma activity ofD. chrysotoxum, five key compounds and nine key targets were obtained through constructing and analyzing the compound-target-pathway network. The five key compounds were chrysotobibenzyl, chrysotoxin, moscatilin, gigantol and chrysotoxene. Nine key targets, including GAPDH, EGFR, ESR1, HRAS, SRC, CCND1, HIF1A, ERBB2 and MTOR, could be considered as the core targets of the anti-hepatoma activity ofD. chrysotoxum.ConclusionsIn this study, the chemical composition difference and anti-hepatoma activity of stems and leaves ofD. nobileandD. chrysotoxumwere compared, and the potential anti-hepatoma mechanism ofD. chrysotoxumwas revealed in a multi-target and multi-pathway manner.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12906-023-04048-y.