Recent research has increasingly focused on plant-derived products as potential alternatives to chemotherapeutic agents, aiming to reduce side effects. Among these, plant-derived nanovesicles (NVs) have garnered significant attention for their potential in treating colitis. In this study, we extracted NVs from the leaves (LNVs) and stems (SNVs) of Taxus, a well-known natural anti-cancer plant. The targeting ability of these NVs was evaluated in the mouse colon using an IVIS imaging system. Additionally, we assessed the therapeutic effects of these plant-derived NVs on ulcerative colitis in a mouse model. Our findings reveal that the NVs exhibit an ideal vesicle size of 150.0 nm and contain a rich array of lipids, functional proteins, and bioactive small molecules. In vitro anti-inflammatory experiments demonstrated that both LNVs and SNVs enhanced cell viability and reduced levels of pro-inflammatory cytokines. Importantly, neither LNVs nor SNVs induced significant cytotoxicity. In vivo, oral administration of LNVs and SNVs ameliorated colitis-related symptoms in mice and accelerated colitis resolution by suppressing the TLR4/MyD88/NF-κB pathway and reducing levels of pro-inflammatory cytokines, including IL-1β, IL-6, and TNF-α. Furthermore, 16S rDNA sequencing data suggested that LNVs play a crucial role in regulating gut microbiota. Collectively, our findings suggest that plant-derived NVs from Taxus represent a promising novel natural nanomedicine for use as an anti-inflammatory agent in the treatment of colonic diseases.