A preprocessing program for a distributed hydrological model is very important because it will greatly influence the results of runoff simulation. Runoff simulations include several procedures, such as the determination of flow directions, definition of runoff routing orders, estimation of flow accumulation areas and extraction of drainage networks, etc. In order to simplify the development work and to improve the efficiency of model development, a preprocessing program was developed that can work independently with a graphic user interface. Only digital elevation model (DEM) data are required in this program and characteristics of the program include the following components: (1) a method for the determination of flow direction without sink filling; (2) a leaf clipping method for watershed partitioning; and (3) the determination of the order of runoff routing according to a top-down method. Finally, a case study in the Lhasa River basin is presented, and three case studies in the Wei River, Zhangweinan River and Sanchuan River basins are selected to validate the program. The results show that disconnected or parallel drainage networks can be avoided by using the preprocessing program, especially in flat areas, which can significantly improve the development of distributed hydrological models.