Bitter melon (Momordica charantia L.) is a unique vegetable-fruit possessing several multifarious health benefits. In this study, the plant extraction obtained from grafted bitter gourd onto pumpkin (Cucurbita maxima) and nongrafted bitter gourd cultivated under greenhouse conditions were evaluated for their constituents of volatile compounds. Gas chromatography-mass spectrometry (SPME-GC-MS) techniques were employed to determine these compounds in the leaves (young, middle, and old-age) and fruits (unripe and ripe) of bitter gourd. The volatile compounds in the leaves of pumpkin during the three stages mentioned above were also investigated. Overall, 72 in leaves and 56 in fruits of bitter gourd compounds belonging to eight major chemical groups were identified: acid, alcohol, aldehyde, alkane, ester, ketone, lactone, and terpene. A total of 52 compounds belonging to the eight major groups mentioned above were also identified from pumpkin leaves. Aldehyde, terpene, and ester were reactively the most prevalent groups found in bitter gourd and pumpkin. The grafted bitter gourds developed up to 23 new compounds in leaves and 15 in their fruits. The grafting of bitter gourd onto pumpkin also halted the production of up to 15 different compounds in fruits and seven in their leaves. Based on principal component analysis and cluster analysis results, the dissimilarity between grafted and nongrafted bitter gourd decreased over time from young to old leaves or unripped to ripe fruit. In conclusion, the grafting of bitter gourd onto pumpkin drastically reshaped the composition of volatile compounds in both leaves and fruits of bitter gourd.