This study used seeds-watermelon seed protein as research object, and the effects of lipid per oxidation product, Malondialdehyde (MDA) on its structure and gelling properties were investigated by means of circular dichroism spectroscopy and texture analyzer etc. The results showed that the surface hydrophobicity of seeds-watermelon seed protein decreased from 10 229 to 2 459, and the β-sheet content in the secondary structure increased, and the irregular curl content decreased; the oxidation of MDA made the gelling strength of seeds-watermelon seed protein gradually deteriorate, the water-holding capacity first decreased and then increased, and the oil-holding trend was opposite; when the concentration of MDA reached 0.1 mmol/L, the water-holding capacity of seeds-watermelon seed protein reached the minimum value of 174.5%, and the oil-holding capacity reached the maximum value of 404.5%. The study indicated that mode-rate oxidation was beneficial to functional properties of seeds-watermelon seed protein.