This study aimed to develop a green and efficient approach based on pulsed electric field (PEF) in combination with deep eutectic solvents (DESs) to enhance the antiglycation ability of Noni flavonoids (NFs) by modulating their proportions of flavone glycosides and aglycones. The results showed that the proportion of quercetin was elevated with the increasing PEF treatment times at fixed treatment conditions (PEF conditions: 2 kV/cm, 30 μs, 10 Hz; DES: 100% choline chloride/oxalic acid). After 4000 PEF treatments, the molar ratio of rutin and quercetin in the NF sample changed from 0.92:0.08 to 0.09:0.91. Simultaneously, the inhibitory effects of the NF sample treated with 4000 pulses (NF4) on fructosamine, α-dicarbonyl, and advanced glycation end products (AGEs) in the bovine serum albumin (BSA)−fructose model were increased by 2.53, 2.98, and 1.23 times, respectively. This enhancement may be attributed to NF4 exhibiting a greater ability to bind protein and trap methylglyoxal (MGO) compared with untreated samples. Consequently, NF4 can more effectively prevent oxidative damage to the BSA structure, reducing protein aggregation and blocking the accumulation of AGEs. In summary, the combination of PEF with DESs presents a promising and sustainable method to effectively improve the antiglycation ability of Noni flavonoids, showing great potential for the functional food industry.