Abstract: To decipher the key bitter compounds affecting the taste of fresh lotus seeds and the differences between cultivars, this study employed untargeted metabolomics to compare lotus plumule at the waxy ripeness stage from the cultivars ‘Hangpanguolian 1' and ‘Jianxuan 17'. The results showed that a total of 74 differentially expressed metabolites were identified, of which 28 were successfully matched to the KEGG database. KEGG pathway analysis indicated that these metabolites were enriched in pathways such as nicotinate and nicotinamide metabolism, carbon fixation by Calvin cycle, alanine, aspartate and glutamate metabolism. By examining the accumulation patterns of benzylisoquinoline alkaloids(BIAs), we found that the abundances of 14 key compounds along the BIA biosynthetic pathway from dopamine to liensinine, nuciferine, and etc. were consistently and significantly lower in Hangpanguolian 1 than in Jianxuan 17. This systemic downregulation constitutes the core chemical basis for the lower perceived bitterness in Hangpanguolian 1. The study provides a metabolic-level explanation for the formation of the low-bitterness trait in fresh lotus seeds, offering theoretical support for breeding specialized cultivars.