HPLC was used to separate and determine the content in natural brown cotton fiber of flavonoids such as myricetin,quercetin,naringenin and kaempferol colored cotton.The result showed that the four kinds of flavonoids were separated completely,with the average rate of recovery of 96.3% ~99.3%.The sample may be kept stable in 10 hours.The output of myricetin,quercetin,naringenin and kaempferol in brown cotton fiber is 44.68,28.2,47.2,64.6 ng·g-1 in fresh weight,respectively.