Abstract BACKGROUND Flowering Chinese cabbage is a popular Brassica vegetable valued for its nutritional properties. However, the impact of common processing methods on its bioactive components and their associated biological activities remains unexplored. Understanding these shifts is crucial for maximizing its health benefits during consumption and industrial production. This study investigated how the bioactive ingredients in flowering Chinese cabbage were impacted by three typical processing methods: steaming, hot‐air drying, and freeze‐drying. Their methanol extracts for preventing the proliferation of colon cancer cell line HT29 were assessed. Component shifts and potential bioactive components responsible for the observed effects were found using untargeted metabolomics and network pharmacology analysis. RESULTS The results show that, in contrast to the steamed group, both drying methods (hot‐air drying and freeze‐drying) demonstrated significant inhibition of HT29 cell proliferation at 1000 μg mL −1 . Metabolomic analysis revealed that cinnamic acids and derivatives, flavonoids, and prenol lipids were the primary metabolite categories significantly altered by all three processing methods. Given the superior inhibitory activity of both drying groups, network pharmacology analysis pinpointed specific differential metabolites (sulforaphane, pentamidine, S‐adenosylhomocysteine, and S‐adenosylmethionine) enriched in both drying groups as potential key contributors to the anti‐proliferative. CONCLUSION This study provides clear evidence that processing methods significantly alter the bioactive component profile and associated anti‐cancer potential of flowering Chinese cabbage. Drying processes, in particular, enhance specific bioactive metabolites linked to potent HT29 cell inhibition. These findings offer valuable insights for selecting processing methods to preserve or enhance the health‐promoting properties of this vegetable. © 2025 Society of Chemical Industry.