Abstract: The content changes of rutin, isoquercitrin, and quercetin from different medicinal parts of Toosendan Fructus in different harvest time were compared. The chromatographic separation was performed on a Agilent zorbax SB-C18 column (4.6mm×150mm, 5μm) kept at 25℃ using methanol-acetonitrile (volune ratio 1:10)(A) and 0.4% phosphoric acid solution (B)as the mobile phase at a flow rate of 1.0mL/min through gradient elution and the detection wavelength at 360 nm. The contents of rutin, isoquercitrin, and quercetin from Toosendan Furctus in different harvest time were greater differences. The results showed that the content of rutin was the highest among these three flavonoids. The rutin contents from fruit of Toosendan Fructus were 43.80, 62.64, 117.20, 90.89 and 87.13 μg/g in different harvest times. The contents of three flwvonoids were large changes with different growth period. It showed increased and then decreased trends. The total amount of these three flavonoids was the largest in January. They were 199.11, 133.78, 133.81 and 23.55 μg/g from different medicinal parts of Tossendan Fructus. In the same harvest time, the amount of these three flavonoids in the fruit pulp and core were higher than those in the other parts of Toosendan Fructus. In different harvest times, the total content of the three flavonoids were 5.81, 42.44, 133.78, 156.44 and 135.80 μg/g in the pulp, and 48.53, 77.99, 133.81, 125.45 and 116.88 μg/g in the core.