A metabolomics-flavoromics approach was conducted to assess the micromolecules of ‘Nam Dok Mai Si Thong’ and ‘Nam Dok Mai No. 4’ mango cultivars from two seasons. During ripening, FAMEs, FFAs, fatty alcohols, sterols, and organic acids were dominant at 0–2 days, whereas amino acids, sugars, and volatile organic compounds, including esters, alcohols, ketones, aldehydes, and terpenes, were at higher levels at 4–8 days. Nine metabolites (palmitic/linoleic/linolenic/citric/malic acids, β-sitosterol, sucrose, glycine, and leucine) and two volatile organic compounds (ethyl octanoate/decanoate) were related to ripening-associated changes within eight days. During ripening, sucrose at 6–8 days, citric/malic acid at 0–2 days, glycine and leucine at 4 days, and ethyl octanoate and ethyl decanoate at 8 days could be used as quality biomarkers for Nam Dok Mai Si Thong; palmitic/linoleic/linolenic acids at 0 days and β-sitosterol at 0–4 days could be used as quality biomarkers for Nam Dok Mai No. 4.