Quercetin (Que), kaempferol (Kaem), isorhamnetin (Irh), and myricetin (Myri) are typical flavonols that are abundant in plant resources. This research investigated their ability in attenuating harmful glycation product formation and the effect of hydroxyl substitution. The inhibition mechanisms were elucidated by fluorescence spectroscopy and nano-liquid chromatography Orbitrap tandem mass spectrometry. The results indicated that the 3′-OH on the B-ring is critical in alleviating harmful glycation product formation, methylation reduced its inhibition, and the 5′-OH showed much less contribution than the 3′-OH. Que showed the strongest suppression on initial product, 5-hydroxymethylfurfural, and advanced glycation end product formation, with the corresponding percentage inhibitions at 36.58 μM of 81.1, 56.9, and 95.4%. Que and Myri also clearly inhibited fructosamine and acrylaminde production, while no suppression was observed by Irh and Kaem. The number of glycated sites was reduced from ten to seven, five, six, and nine, respectively, when 36.58 μM Que, Myri, Kaem, and Irh was added. Suppressing the conformational changes of ovalbumin induced by glycation, trapping dicarbonyl compounds, altering the microenvironment around tryptophan, and reducing the glycation activity of potential sites were the major inhibition mechanisms. These results suggest that Que and Myri may be promising natural agents for inhibiting harmful glycation and provide theoretical support for the effective screening of natural antiglycation reagents.