The influence of key processing unit operations on the changes in the flavor compounds of NFC (not from concentration, NFC) Bisekxing melon juice by gas chromatography-ion mobility spectroscopy (GC-IMS), so as to provide certain theoretical guidance for its processing. Using the commercially available fresh thick-skinned muskmelon as the experimental material, NFC Bisekxing melon juice was processed through five operation units, fresh squeezing, enzyme inactivation, homogenization, ultrasound treatment and sterilization. GC-IMS was used to analyze qualitatively the flavor substances in the melon juice samples obtained after the processing step of each operation unit, and three-dimensional and two-dimensional topographic maps and fingerprints of the melon juice samples were constructed along with PCA analyses. The results showed that a total of 61 volatile substances belonging to 35 kinds of volatile substances were detected in the NFC Bisekxing melon juice, including 7 kinds of aldehydes, 9 kinds of alcohols, 10 kinds of hydrocarbons, 5 kinds of ketones, and 4 kinds of esters. Enzyme inactivation exerted the greatest impact on the flavor substances of melon juice, causing the melon juice to produce odor substances such as benzaldehyde, while promoting the formation of main aroma substances such as ethyl propionate. The flavor of melon juice after enzyme inactivation was significantly different from that of melon juice treated by other processing units. The main aroma substances of melon juice were aldehydes and esters. Other key processing unit operations hada certain influence on the flavor substances in melon juice. These results provide a theoretical basis for controlling the processing parameters in the preparation of NFC Bisekxing melon juice and improving the quality of melon juice.