Abstract: Animal-derived medicines, with a long clinical history and unique therapeutic effects, are rich in proteins and peptides, yet their compositional analysis remains challenging. Bungarus Parvus, used for meridian dredging, is typically administered in juvenile form, but a scientifically defined cultivation window has remained unclear. We conducted, for the first time, a multi-omics comparison of proteins, native peptides, amino acids, and nucleosides across five developmental stages (7-15 days; 4, 8, 16, and 20 months). Using a theoretical protein database, 374 high-confidence proteins and 4,989 peptides were identified, and 4 amino acids and 5 nucleosides were quantified. The 7-15 days stage exhibited a more abundant and distinctive chemical composition. Multi-omics analyses consistently separated it from ≥4 months, suggesting 7-15 days as the preferred harvest stage. To verify proteins and peptides identification, 7 special peptides were synthesized, and quantified via a validated LC-MRM method. P4 was exclusive to 7-15 days samples, while P2 ( ~ 2% of total content) showed a ~ 30-fold difference between 7-15 days and later stages, serving as robust markers. Additionally, 7 native peptides, glycine (1.25%), hypoxanthine (0.06%) were identified as complementary markers. This work presents the first chemical portrait of B. Parvus, clarifies its optimal harvest window from a chemical perspective, and offers a framework for other animal-derived medicines.