To overcome bioavailability limitations of traditional anti-cancer phytochemicals, we engineered exosome-delivered Salidroside component (EDSC) and mechanistically dissected its therapeutic efficacy against aggressive breast cancers. In vitro and in vivo models evaluated EDSC’s phenotypic impact. Integrated transcriptomics/proteomics uncovered molecular targets, validated through CRISPR/Cas9-generated CDKN2D (Cyclin-Dependent Kinase Inhibitor 2D) mutants and AKT inhibitor assays. Direct binding was resolved via molecular docking, Covalent Binding Assay Coupled with Mass Spectrometry, and Fluorescence Resonance Energy Transfer assays. Rescue validation was conducted on both transiently and stably transfected cell lines harboring site-directed mutations. EDSC exhibited superior tumor accumulation and cytotoxicity versus free Salidroside, suppressing proliferation, cell cycles (G1/S phase), and migration. Multi-omics identified CDKN2D upregulation as a key downstream mediator, with Salidroside binding specifically to R40/M50/A17 residues—structurally stabilizing CDKN2D to decrease CDK4/6/CCND1 complexes. Molecular dynamics simulation analysis verified the critical binding site of R40-mutation in CDKN2D with Salidroside. Simultaneously, EDSC inhibited CDK1 (Cyclin-dependent kinase 1) through PI3K/AKT inhibition independent of CDKN2D. CRISPR-mutagenesis of binding residues abolished EDSC’s effects, while MK-2206 co-treatment enhanced G1/S arrest via synergistic dual-pathway blockade. EDSC represents the molecularly resolved, inducing aberrant conformations of CDK4/6/CCND1, resulting in cell cycle arrest. Moreover, EDSC also possesses a inhibiting effect of phosphorylated-CDK1 via PI3K/AKT signaling pathway.