• NaBH 4 was identified as novel and effective method to degrade melanoidins. • NaBH 4 produced typical polymers with an MW difference of 74 Da. • The mechanism of the formation polymer was elucidated. • Matching MW of theoretical and experimental polymers validated the pathway. • The polymers could be a candidate biomarkers for melanoidins. Melanoidins, are of increasing interest for their potential biological activities. However, little knowledge is available on their structure. In the present study, vinegar, coffee and model melanoidins were degraded by NaBH 4 , and the resultant reaction products were characterised by chromatography, mass spectrometry and spectrometry methods to elucidate the mechanism of formation of melanoidin skeleton molecules. The study identified a typical polymer with a molecular weight (MW) interval of 74 Da, which was polymerised by aldol condensation and reduced by NaBH 4 , followed by intermolecular dehydration. MW of the theoretically derived typical polymers matched the detected polymers, validating the speculated pathway involved in the formation of melanoidins skeleton molecules. The study also revealed that melanoidins from different sources contain polymers with the same MW and different binding preferences, contributing to the heterogeneity of melanoidins. Overall, these findings indicated that the identified polymers could be used as potential candidate biomarkers for melanoidins.