Abstract: Constant head and flux boundaries are widely used upper boundaries of numerical simulations, which is however beyond the actual conditions. The differences between the two methods and their applicable conditions were compared in this study. Formation and controlling mechanisms of water table were discussed using an analytical method and an improved numerical simulation method of variable upper-boundaries was proposed. The formation and influencing factors of the northern Ordos Basin cretaceous groundwater flow systems was analyzed as a case study. The results show that water table of the northern Ordos Basin cretaceous flow systems was controlled by three factors including terrain, recharge conditions and hydraulic conductivity. Specific local climate, topography and aquifer lithology effect the development and evolution of groundwater flow systems by controlling water table. The numerical simulation method of variable flux upper-boundaries applied to analyze the impact of upper-boundaries changes on groundwater flow systems at basin scales is an effective way for deeply understanding the formation and evolution mechanisms of regional groundwater flow systems as well as for identifying the interaction between groundwater systems and climatic variations and vegetation changes.