Lysine (Lys) glycated by xylose (Xyl) at α-NH2 [Nα(1-deoxy-D-xylulos-1-yl)lysine (Nα-Xyl-Lys ARP)] or ε-NH2 [Nε-(1-deoxy-D-xylulos-1-yl)lysine (Nε-Xyl-Lys ARP)] significantly impacted the thermal degradation pathways of Amadori rearrangement products (ARPs). Nα-Xyl-Lys ARP was found to undergo retro-aldolization on the sugar fragment more readily to form glyoxal/methylglyoxal than Nε-Xyl-Lys ARP. Furans and pyrazines formation during the degradation of the diglycated lysine [Nα,Nε-di(1-deoxy-d-xylulos-1-yl)lysine (Nα,Nε-di-Xyl-Lys ARP)] was delayed at 120 °C relative to Nε-Xyl-Lys ARP. This was attributed to the complex degradation of Nα,Nε-di-Xyl-Lys ARP, which slowed the substantial formation of deoxypentosones and the effective release of Lys. At 140 °C, the dual glycated Nα,Nε-di-Xyl-Lys ARP was more conducive to promoting the redistribution of electrons and facilitating molecular rearrangement. This accelerated the efficient decomposition of dual glycated groups in Nα,Nε-di-Xyl-Lys ARP and enabled glyoxal to actively participate in Strecker degradation. Thus, the production of furans and pyrazines was substantially increased, and the variety of pyrazines was expanded from three types to eight types. An appropriate increase to pH 7.5 effectively avoided the overprotonation of hydroxyl and amino groups (pH 5.5), simultaneously enhancing furans and pyrazines yield while minimizing the formation of pyridines under alkaline conditions.