Cadmium (Cd), a highly toxic non-essential heavy metal, disrupts cellular processes even at low concentrations. The current studies of Cd stress rely on whole-plant models with prolonged treatments, obscuring early response signals. Tobacco, a typical model plant, lacks protoplast-level investigations under Cd stress. Here, we integrated SWATH-based LC-MS proteomics and GC-MS metabolomics to resolve early Cd-responsive mechanisms in tobacco protoplasts, uniting bioinformatics analyses (WGCNA, k-means, PPI networks). 3262 proteins and 131 primary metabolites were identified. The hub proteins (ROS scavengers, protein synthesis) and differentially expressed metabolites, transient monosaccharide depletion (15 min) followed by recovery, and sustained organic acid accumulation-were characterized. The results indicate rapid energy and some metabolites were supplied via glycolysis and the TCA cycle to alleviate oxidative damage and enhance stress protein synthesis. This study results deciphers tobacco's multi-omics defense strategy against Cd stress, filling knowledge gaps in early stress signaling. In the future, we anticipate that our study will contribute to advancing protoplast omics.