To estimate the quality of mussels during storage, the mortality, succinate dehydrogenase (SDH) activity, extractive components, viable bacterial count (VBC), and bacterial flora of live mussels were investigated. The hierarchical cluster analysis, based on extractive components and VBC, taste active value (TAV), and equivalent umami concentration (EUC), suggested that metabolite composition, bacterial, and taste changing patterns of samples stored at 5 and 10°C differed from those stored at 0°C. The mortality of mussels stored at 5 and 10°C was lower than those at 0°C. The gills of live mussels stored at 0°C for more than 7 days exhibited significantly lower SDH activity than those stored at 5 and 10°C. There was no significant difference in EUC among the samples stored at different temperatures, but a significantly higher TAV of Ala and succinic acid was observed in live mussels after 12 days of storage at 5 and 10°C than in those stored at 0°C. Next‐generation sequencing analysis showed that samples stored at 5 and 10°C lost bacterial diversity, and their bacterial flora changed compared to that before storage. Considering these results, the most suitable storage condition to maintain high quality for live mussels is 5°C for less than 7 days.