Aquifer heterogeneity is an important factor influencing regional groundwater flow patterns. The complex structural and stochastic characteristics of regional-scale aquifer heterogeneity are difficult to characterize, which leads to insufficient understanding of the effects of heterogeneity on groundwater flow systems in practice. In this paper, the Cretaceous groundwater flow system in the Ordos Basin is studied based on the selected typical geological section. Stochastic numerical simulation of the two-dimensional section is employed to analyze the influence mechanism of aquifer layered heterogeneity on groundwater flow systems by comparing the changes of the groundwater flow field under different heterogeneity conditions. The results show that the groundwater flow net is close to the actual conditions when the ratio of horizontal to vertical conductivity (Kh/Kv) is 1000 in model for homogeneous aquifer. It is close to the actual conditions when the variance of conductivity is 0.91, the horizontal correlation length is 5000 m and Kh/Kv is 150 for heterogeneous aquifers. The stochastic simulated aquifer generated by three parameters (i.e., horizontal correlation length, variance of permeability coefficient, and anisotropy ratio) can well characterize the layered heterogeneity of aquifer and its influence on the groundwater flow systems. Due to the superposition of layered heterogeneity at different scales, equivalent homogeneous, anisotropic model for conceptualizing layered heterogeneous medium in large-scale groundwater flow simulation may lead to a much larger horizontal-to-vertical anisotropy ratio than the ratio between horizontal and vertical correlation scales.