Despite the high nutritional value and active components present in mungbean sprouts, the influence of different accessions on their nutrition remains unclear. Two accessions with pronounced differences in germination experiments were selected in this study, as the average fresh weight and root length of Shilv 22 (SL22) seedlings were only 47% and 41% of those of Shilv 17 (SL17), respectively. In order to investigate the metabolic changes that occur during mungbean germination, nontargeted metabolomics was performed with different accessions of mungbean sprouts. The results revealed that SL17 and SL22 accessions had extreme differences on metabolic changes, and amino acids including tyrosine, proline, aspartate and asparagine were considered to serve as potential markers to distinguish the two accessions. SL17 accumulated more vitamin B, flavonoids and phenolic acids than SL22 mungbean sprouts after 60 h, a critical time point of germination. Network pharmacology analysis indicated that caffeic acid, naringenin, kaempferol, apigenin and pinocembrin could be potentially used as crucial active components of mungbean sprouts for future research. This study offers a strong theoretical foundation for producing cost-effective, highly nutritious mungbean sprouts in the market.