This paper studied a method of partitioning water year, wet season and dry season (WWD), so as to provide a scientific basis for the hydrological and hydraulic calculation of river basin. Initially, the cumulative anomaly of runoff time series was used to formulate the partition method of WWD on the basis of runoff characteristics. The upstream of the Heihe River Basin was taken as an example to validate the proposed method. The results show that the method determined the reasonable WWD of the river basin. In addition, the statistical properties of runoff time series and intra-annual runoff distribution of typical year had significant changes under different starting-and-ending time of water year. Therefore, the proposed partition method could be applied to determine WWD of a river basin, and unifying the partition method of water year is quite essential for the hydrological and hydraulic calculation.