The plastron of yellow pond turtles is a kind of high-value Chinese herbal medicine with abundant protein resources. Turtle plate has the potential of anti-inflammation, analgesia, enhancing immunity, nourishing yin and suppressing yang, osteoporosis and so on, and is often developed and utilized as a functional food. However, the cartilage protective activity of yellow pond turtle peptides (YPTP) in knee osteoarthritis (KOA) and the associated mechanism have not been reported. Thus, this study investigated the therapeutic potential of YPTP for KOA and HPLC-QTOF-MS identified the structure of peptides. The results revealed that YPTP exhibited significant therapeutic effects against KOA progression. It was found that COX-2 and iNOS were the primary target proteins of YPTP in KOA. Molecular docking analysis further validated the 5 different YPTP-derived peptides that interacted with COX-2 and iNOS via hydrogen bonding and hydrophobic interactions. Using an animal model, we revealed that YPTP significantly suppressed the contents of COX-2, iNOS, and MMP-3 while upregulating COL II to alleviate inflammation and minimize cartilage damage. However, reduced YPTP dose enhanced IL-1β contents in synovial membranes, which requires further exploration.