Objective: This study aimed to explore the effect of processing methods on the quality of pumpkin seed kernels. Methods: In this study, pumpkin seed kernels were chosen as the research object and the effects of air-frying (160 ℃, 0~7 min) and microwave treatment (700 W, 0~7 min) on the physical and chemical properties of proteins were investigated. Results: The experimental results showed that: after air-frying and microwave treatment, polyphenol, flavone, polysaccharide contents, as well as sensory scores all increased at the beginning, then decreased gradually, and reached the peak values when being treated by air-frying for 4 min and microwave treatment for 5 min, respectively. Under the optimal conditions, the degree of lipid oxidation was lower after microwave treatment, the protein aggregation phenomenon was more obvious, and the structure tended to be disordered and stretched, with a higher degree of lipid oxidation and better digestibility, while air-fried nuts had a stronger roasted flavor. Conclusion: The results indicated that proper air-frying and microwave treatment could improve the flavor and digestive properties of pumpkin seed kernels, and then improve the quality of pumpkin seed kernels.