Mono Trap has the characteristics of large extraction amount and simple operation. It has the advantages in the extraction of odor compounds in watermelon juice. Mono Trap and thermal desorption combined with gas chromatography-olfactory-mass spectrometry were used to extract and analyze the odor compounds of watermelon juice before and after thermal treatment. The three adsorbent materials, RGC18, RSC18 and RGPS, were used and identified 50 and 71 odor compounds from fresh and heated watermelon juice, respectively. The comparison results of the extraction effects of these three adsorbent materials showed that RGC18 had the best extraction effect on the odor compounds of watermelon juice. 41 and 53 odor compounds were extracted by RGC18 from fresh and heated watermelon juice, respectively. After the thermal treatment, the odor compounds of watermelon juice have changed greatly. The odor activity value of compounds exhibited bitter almond, soapy, and sharp acidic flavors, such as 2-methylbutanal, furfural, octanal, decanal, (E)-2-heptenal, acetic acid and formic acid increased, while hexanal, β-cyclic citral and (E,E)-2,4-nonadienal with green and lemon odor cannot be smelled. The changes of these compounds were the important reasons for the off-flavor of watermelon juice after thermal treatment.