Cucumber is a widely consumed vegetable crop known for its rich nutrient composition and distinctive flavor, influenced by both volatile and non-volatile compounds. Grafting and delayed harvesting are crucial strategies for increasing cucumber yield. The present study investigates the impact of delayed harvesting at different developmental stages and grafting on the metabolic profile, flavor, and overall quality of cucumber fruits Yuxiu 2 (YX) using UPLC-MS/MS and GC-MS/MS techniques. The results indicate that delayed harvesting of YX led to significant increases in length, diameter, and weight from 12 to 24 days after pollination (DAP), with minimal growth beyond 24 DAP. However, grafting did not affect these physical parameters compared to self-rooted plants. Furthermore, metabolic profiling reveals that delayed harvesting enhances the concentration of certain non-volatile metabolites, including alkaloids, organic acids, and phenolic acids, while leading to a reduction in flavonoid contents. Overall, 140 non-volatile and 26 volatile differential metabolites were screened at three developmental stages. Notably, four new organic acids (6-amino hexanoic acid, 5-amino valeric acid, 1-hydroxy2-naphthoic acid, and succinic semialdehyde) and three novel alkaloids (3-indole acetonitrile, epinephrine, and serotonin) were identified. Volatile compounds, such as aldehydes, esters, terpenes, alcohols, and ketones, exhibit a peak in concentration at 24 DAP, followed by a decline. The characteristic cucumber flavor compound, (E,Z)-2,6-nonadienal, remains consistent across all developmental stages. In grafted cucumber fruits, a total of 113 non-volatile and 11 volatile differential metabolites were screened, and among them, ten unique non-volatile metabolites were detected in grafted fruits, contributing to the sour and bitter taste of cucumbers. Moreover, some of the metabolites like (1S,4S,4aR)-1-isopropyl-4-methyl-7-methylene-1,2,3,4,4a,5,6,7-octahydronaphthalene with pentylenetetrazol contribute to an undesirable camphor-like odor. The study concludes that while delayed harvesting and grafting practices can increase cucumber yield, they also significantly alter the fruit's metabolic profile, impacting taste and flavor.