Increasing evidence has identified α-dicarbonyl compounds, the reactive intermediates generated during Maillard reaction, as the potential factors to cause protein glycation and the development of chronic diseases. Therefore, there is an urgent need to decrease the levels of reactive dicarbonyl compounds in foods. In this study, we investigated the inhibitory effect of quercetin, a major dietary flavonoid, and its major mono- and di-MGO adducts on the formation of dicarbonyl compounds, such as methylglyoxal (MGO) and glyoxal (GO), in a lysine/glucose aqueous system, a model system to reflect the Maillard reaction in food process. Our result indicated that quercetin could efficiently inhibit the formation of MGO and GO in a time-dependent manner. Further mechanistic study was conducted by monitoring the formation of quercetin oxidation and conjugation products using LC-MS/MS. Quercetin MGO adducts, quercetin quinones, and the quinones of quercetin MGO adducts were detected in the system, indicating quercetin plays a dual role in inhibiting the formation of MGO and GO by scavenging free radicals generated in the system and trapping of MGO and GO to form MGO adducts. In addition, we prepared the mono- and di-MGO quercetin adducts and investigated their antioxidant activity and trapping capacity of MGO and GO. Our results indicated that both mono- and di-MGO quercetin adducts could scavenge the DPPH radical in a dose-dependent manner with >40% DPPH scavenged by the MGO adducts at 10 μM, and the di-MGO quercetin adduct could further trap MGO to generate tri-MGO adducts. Therefore, we demonstrate for the first time that quercetin MGO adducts retain the antioxidant activity and trapping capacity of reactive dicarbonyl species.