Three alternative groundwater flow models were evaluated for Beijing Plain, China. The first model (AM1) was constructed with the “thin layer approach” in which all 9 model layers, including five aquifers separated by four aquitards, are continuously present in the same model area. The second model (AM2) was constructed with the “quasi-3D approach” in which the hydrogeological formations were classified into five aquifer units consisting of mixed permeable and semi-permeable layers at different depth ranges. The third model (AM3) was constructed with the “true layer approach” in which aquifers and aquitards were defined according to hydrostratigraphic properties, and model layers are absent in the area where corresponding hydrogeological formations intersect bedrocks. All 3 models were calibrated with the parameter optimization method under the steady state flow condition with the same hydrological stresses and observation data. All three models fit to observations well with the similar calibration criteria values. Furthermore, AIC and BIC information criteria could not distinguish three alternative models. Only KIC could identify AM3 as the best model. Major differences of the three alternative models were identified from a hydrogeological perspective. The AM1 model depicted an illusion through contour maps that groundwater was present everywhere in the deep aquifers. The model computed larger vertical leakages because more abstraction rates were assigned improperly in deep aquifers. The AM2 model was able to compute regional groundwater balances and depicted spatial groundwater level variations. However, the AM2 model computed longer groundwater travel times around the wellfield and should not be used for the delineation of the well field protection zones and contaminant transport simulation. The AM3 model could not only compute the regional groundwater balances and describe spatial groundwater distribution in deep confined aquifers, but also delineate the capture zone of the wellfield. It can therefore be used for simulating contaminant transport. Furthermore, the AM3 model is suitable to construct a coupled regional and local flow model for simulating a managed aquifer recharge scheme.