The paper presented a method to divide the variation of high and low flow by using the Mann-Kendall method. Firstly, a runoff time series were divided into several time series, and then, the U values of the series were calculated to obtain. Finally, the variation process of high and low runoff was determined according to the U-t curve. The runoff series of Zhuqi gauge station in the Minjiang River watershed and Baishan reservoir were analyzed as example. The results showed that the annual stream flow sequence with variation process of high and low runoff was 1946to 1996in the Mingjiang River.The variation of high and low runoff in the Baishan reservoir was 1946to 1966and 1967to 1975respectively, and the third variation one wasn''t completed up to now. The result also showed that the Mann-Kendall method was applicable in dividing the variation of high and low runoff.