Agricultural production is threatened by waterlogged and soil salinization due to the flat relief, concentrated rainfall in summer, shallow ground water and high salinity in the Yellow River delta, construction of drainage systems thus becomes a prerequisite for production of food and cotton in this area. As the current standards for subsurface drainage design are developed on the basis of average soil moisture condition, the stochastic nature of the hydrological process and the special feature of the regional hydrological factors are neglected. This paper studied the effects of subsurface drainage systems layout with the field hydrology model-DRAINMOD. The results showed that shallow drainage may better perform on water control of farmland, non-point source reduction and sea water intrusion prevention than the traditional deep drainage ditches in the study area. The simulated total drainage discharge was significantly less with the shallow subsurface drainage layout than with the traditional deep ditch system. The results may provide practical guidance for agricultural production and ecological environment protection in the Yellow River Delta.