Flavonoids (dihydromyricetin, dihydroquercetin, epicatechin, and epigallocatechin) were applied to indicate the critical formation condition of the Amadori rearrangement product (ARP) in Maillard reaction performed under a two-step temperature rising process in the threonine−xylose model system. Threonine-ARP (Thr-ARP) was mixed with dihydromyricetin (DM), dihydroquercetin (DQ), epicatechin (EC), and epigallocatechin (EGC) before the heat treatment; then, the mixture was tested by liquid chromatography−mass spectrometry (LC−MS). The results showed that these flavonoids trapped the ARP and generated adducts. The A-ring of flavonoids (the meta-polyhydroxylated benzene ring) was the functional group to capture the Thr-ARP. The relative contents of the adducts of DM-Thr-ARP, DQ-Thr-ARP, EC-Thr-ARP, and EGC-Thr-ARP were compared with each other, and it was found that the structure of the C-ring of the flavonoids (the carbonyl group on C-4) significantly impeded the formation of adducts with Thr-ARP, while the number of hydroxyl groups on the B-ring had little influence. The formation of adducts delayed the degradation of Thr-ARP, decreased the production of α-dicarbonyl compounds, and suppressed Maillard browning. In this way, the flavonoids might trace the critical formation conditions of ARP during the two-step temperature rising process.