Objective: This study aimed to explore the differences in the aroma of watermelon seeds under different thermal processes. Methods: The analysis technics such as Headspace-Solid Phase Micro Extraction-Gas Chromatography-Olfactory-Mass Spectrometry (HS-SPME-GC-O-MS) and Electronic Nose (E-nose) were applied. Results: Thermal processing changed the flavor of watermelon seeds from light fragrance to strong roasted flavor; A total of 18 categories including 115 volatile compounds were detected with the help of HS-SPME-GC-O-MS, among which pyrazines, alcohols and aldehydes accounted for 34.25%, 21.07% and 10.99% of the total volatile compounds, respectively; In addition, 63 volatile compounds were discovered in watermelon seeds after microwave treatment, and pyrazines accounted for 53.31% among all these volatile compounds. Conclusion: Thermal processing treatment showed significant influence on the aroma of watermelon seeds, and the aroma of watermelon seeds after microwave treatment was more intense than air-frying and baking treatment.