Seed watermelon kernel is a typical complex food with high fat and protein contents. During storage and processing, it is often affected by various factors to undergo interactions between components, which lead to its quality change. In this experiment, seed watermelon kernels were used as research objects, and the effects of 2 -Azobis (2-amidinopropane) dihydrochloride (AAPH) on seed watermelon kernel protein isolates (WMP) were investigated. The structure and digestion characteristics of WMP after oxidation were studied. The results showed that with the increase of AAPH concentration (0.05−5 mol/L), WMP showed obvious aggregation, and its solubility decreased from 6.76 mg/mL to 9.59 mg/mL. The free sulfhydryl content of WMP was 18.24 mmol/g decreased to 11.25 mmol/g, ˛-helix decreased and ˇ-sheet decreased in secondary structure, and its disulfide bond increased by 43.06 mmol/g from 39.57 mmol/g, enthalpy ( H) and denaturation temperature increased (Td) (P < 0.05). By mass spectrometry results of simulated gastric digestion products, it was found that oxidation adversely affected the digestion characteristics of WMP. It can be seen that the lipid oxidation product APPH of seed watermelon kernel can significantly affect the structure and function of the protein extracted from the seed kernel.