•A novel method to construct drainage network considering rice terraces and ponds.•A hybrid vector-raster data model was used for spatial discretization.•Flow direction is determined by elevation and land use specific boundary rules.•The constructed drainage network are more geometrically and topologically realistic.•It is helpful for simulating residence time of water, sediments and nutrients. A well-constructed drainage network is essential for hydrological modeling. Agricultural watersheds with heavy human alternations often contain man-made features like terraced fields and ponds. Incorporating these features in the drainage network in these watersheds is extremely important for hydrological modeling. This study proposed a novel hybrid vector-raster approach to drainage network construction in this type of regions. First, a watershed is discretized using a hybrid vector-raster data model to accurately represent the shapes and areas of irregular geographical entities. Then, the flow directions among discretized units are determined firstly within each land use type and then on the boundaries of different land use types based on elevation and land use specific boundary rules. After that, loops among units are processed to make sure each unit can flow out of the watershed. A small agricultural watershed in Jiangsu Province, China was selected to conduct a case study, and the results showed that the proposed method can obtain a more realistic drainage network than traditional methods, both in terms of geometric shapes and spatial topology.