Flavonoids from plants always show a wide range of biological activities. In the present study, a rapid and highly efficient supercritical fluid chromatography (SFC) method was developed for the separation of 12 flavonoids. After careful optimization, the 12 flavonoids were baseline separated on a ZORBAX RX-SIL column using gradient elution. A 0.1% phosphoric acid solution in methanol was found to be the most suitable polar mobile phase component for the separation of flavonoids. From the viewpoint of retention and resolution, a backpressure of 200 bar and a temperature of 40 °C were shown to give the best results. Compared with a previously developed reverse phase liquid chromatography method, the SFC method could provide flavonoid separations that were about three times faster, while maintaining good peak shape and comparable peak efficiency. This SFC method was validated and applied to the analysis of five flavonoids (kaempferol, luteolin, quercetin, luteoloside, buddleoside) present in Chrysanthemum morifolium Ramat. from different cultivars (Chuju, Gongju, Hangju, Boju). The results indicated a good repeatability and sensitivity for the quantification of the five analytes with RSDs for overall precision lower than 3%. The limits of detection ranged from 0.73 to 2.34 μg/mL, while the limits of quantification were between 2.19 and 5.86 μg/mL. The method showed that SFC could be employed as a useful tool for the quality assessment of Traditional Chinese medicines (TCMs) containing flavonoids as active components.