Plants have developed mechanisms to protect themselves against both biotic and abiotic environmental stress. Specialized/secondary metabolism is one of the stress response mechanisms. Recently, we reported that flavonoids, a class of specialized metabolites, including flavonols and anthocyanins with strong radical scavenging activity contributed to the mitigation of oxidative and drought stress in <i>Arabidopsis thaliana</i> (<i>Arabidopsis</i>). However, the behavior of flavonoids during drought stress is still not well-documented. Herein we investigated the time-series alternation of flavonoids in the aerial part of <i>Arabidopsis</i> (wild type, Col-0) during drought stress by LC-QTOF-MS. The drastic alternation of 5 flavonols and 5 anthocyanins was revealed together with changes in marker metabolites of drought stress, e.g., proline, raffinose, and galactinol. These findings indicate that flavonols and anthocyanins can mitigate drought stress.