• Establishing a multi-level water resource management model applicable in shallow groundwater area. • Considering process-based crops growth model (detailed water and salt movement). • Introducing uncertainties into multi-level programming model. The hierarchical agricultural water resource management problem in shallow groundwater area is expected to be solved through establishing a practical and feasible mathematical model. This study proposes a multi-level programming model with considerations of process-based crops growth model and uncertainties. The model is solved by a fuzzy approach that ensures the decision-making proceeds from top to bottom sequentially and the leader supervises the solution search direction. The leeway given by each level decision maker expands the decision-making space and lets Stackelberg equilibrium solution more satisfactory. The model is applied in Hetao Irrigation District in China. After optimization, the Stackelberg equilibrium water allocation pattern and satisfaction degrees of each level decision makers can be identified. Summarized conclusions are as follows: (1) under uncertainties of available water, the water diversion is allocated in a similar pattern, while the groundwater allocation has larger variabilities; (2) when available water decreases, local farmers can improve crop production through modifying or optimizing irrigation water amount in each growth period; (3) the combined use of water diversion and groundwater is expected to become an effective approach for achieving a win–win situation between government managers and local farmers. The proposed model performs well in generating Stackelberg equilibrium solutions satisfied by multi-level decision makers. It can be extended to provide decision makers a more complete decision support system and also has potential to be applied in other similar areas.