The dried rhizome of Belamcanda. chinensis (L.) DC. is an important traditional Chinese medicine. Previous chemical and pharmacological investigations indicated that flavonoids may be responsible for the bioactivity of the herb. In this paper, the effects on the contents of twelve flavonoids in the three subunit parts of the rhizome of B. chinensis during the thermal drying process under treatment temperatures ranging from 40 °C to 120 °C at 10 °C intervals were investigated. The results showed that the content of most of the individual flavonoids except that of tectorigenin in the fresh eldest parts of the rhizome that originate directly from the seedling was higher than those of the other junior parts. The change trends of flavonoids contents were similar for three subunit parts of the rhizome during the drying process under the same treatment temperature. Most of the individual flavonoid contents in the rhizome increased in the early stages of the drying processes and decreased as the process was prolonged. The durations required to reaching the points of the maximal amounts of flavonoids revealed a significant negative correlation with the temperature. The variation of the content of mangiferin, iristectorigenin A, irigenin, irilone and dichotomitin was positively correlated with irisflorentin that is the chemical marker used for the quality control of this herb. Taking into account of the production effectiveness and flavonoid yields, the appropriate drying temperature for this herb was suggested to be 100 °C.