Controlled drainage by regulating the groundwater level in open ditches is necessary to ensure the normal growth of crops in Northern Huaihe River Plain, China. The groundwater model MODFLOW was calibrated and validated in a representative area, and was then conducted to simulate the groundwater under different main drainage ditch water depth control schemes during the growth period of corn and wheat. Then the scenario with highest water depth (Scenario 20) from 1989 to 2019 was simulated, and the annual cumulative drought and waterlogging intensity (ACDWI) were analyzed in each decade and in different hydrological years. The results showed that the study area was dominated by drought stress. The lowest level of drought stress was achieved under Scenario 20. The frequency of drought gradually decreased from north to south in the study area. Moreover, the ACDWI decreased with increase of precipitation during 1989 to 2019. The results indicated that it was important to store water during the dry season, while it is also necessary to control the drainage in the rainy season to drain excess water on time. The results suggested that the water depth of the main drainage ditch should be regulated by zoning and by season to alleviate crop drought and waterlogging.