Saussurea medusa is a rare traditional Chinese medicinal herb. Besides anti-inflammatory and analgesic activities, it has effects of disinhibiting cold, dispelling dampness and promoting blood circulation. Flavonoids are the main medicinal compounds in S. medusa. Contents of flavonoids and expression of flavonoids biosynthesis related genes in white and red (induced by low temperature, high sucrose and high light) callus were analyzed. The results showed that the total flavone in red line was 3.60 times higher compared to white line. The accumulation of rutin in red line (0.25% of dry weight) was 2.40 times higher compared to white line. Anthocyanins were abundant in red line, with the contents of cyanidin 3-O-glucosidechloride and cyanidin 3-O-succinyl glycoside 0.12% and 0.19% of dry weight respectively. CHS, F3'H, FNS, FLS, DFR and ANS genes were highly expressed in red line compared to white line. Expression of three transcription factors (MYB, bHLH and WD40) in red line was significantly higher than that in white line, especially the expression of MYB (19.70 times higher compared to white line). These results indicated that high expression levels of transcription factors induced high expression of structural genes in red line, thereby enhancing the flavonoids biosynthesis. The expression of bHLH and WD40 was similar, whereas it was significantly different from that of MYB, indicating that bHLH and WD40 could form a binary complex to regulate expression of structural genes and flavonoids biosynthesis.