Durian is an economically important fruit of Southeast Asia. There is, however, a lack of in-depth information on the alteration of metabolic networks during its ripening. Here, we annotated 94 ripening-associated metabolites from the pulp of durian cv. Monthong fruit at unripe and ripe stages, using capillary electrophoresis- and gas chromatography- time-of-flight mass spectrometry, specifically focused on flavor-related metabolites. During ripening, sucrose content was found to be increased. Change in raffinose-family sugars is reported herein for the first time. The contents of malate and succinate increased, while those of citrate, an abundant organic acid, were unchanged. Notably, most amino acids increased, including isoleucine, leucine, and valine, whereas aspartate decreased, and glutamate was unchanged. Furthermore, transcriptome analysis was performed to support the dynamic changes in several flavor-related pathways, and for the identification of key candidate genes. Taken together, our results could be exploited for developing durian metabolic/genetic markers in the future.