Plain farmland areas without significant topographic slope exhibit microtopographic features of different scales. Quantitative assessment of the effects of microtopography at different scales on runoff generation in typical farmland areas is of great significance for regional water resources management and flood disaster forecasting. The main objective of the study was to develop an event-based rainfall–runoff model based on the layered Green–Ampt model (LGAM) with the consideration of plot-scale microtopographic features in plain farmland areas. Our experimental field, located in Taihu Lake Basin, was classified into three types of topographic subunits (i.e., main field, rill, and ditch) according to the average elevation. To simplify the concentration process for three topographic subunits, the average concentration time method was employed. Here, various experimental scenarios were simulated, including two classical unsteady rainfall events in homogeneous soil, one ponding infiltration experiment, and two typical rainfall–runoff events in the experimental field. We found that the multilayered setting showed higher accuracy than the homogeneous setting for simulating infiltration in the ponding infiltration experiment in the field. The RMSE of simulated ponding water depth reduced from 0.166 cm to 0.035 cm and NSE rose from 0.988 to 0.999. The simulated hydrograph considering microtopography effects proved higher accuracy than that under unified topography assumption. After classifying topography, the RMSE and NSE of simulated hydrographs decreased and increased, respectively. The lower the topographic subunit, the earlier the outflow occurred. At the early stage, the runoff mostly originated from the relatively low topographic subunits. Infiltration-excess regime under saturated condition may initially dominate in the low-lying ditch under intense rainfall, with extremely high runoff coefficient. Concentration process in the plain farmland area was affected by both rainfall intensity and microtopography. The greater the rainfall intensity, the shorter the average concentration time. The concentration velocity under heavy rainfall was four times faster than that under light rainfall. The lower topographic subunit was characterized by shorter concentration pathway and average concentration time. Ditches reduced the peak flow and advanced the time to peak. This quantitative study provides new insights into effects of microtopography on runoff generation in plain farmland area as well as an effective alternative for plot-scale rainfall–runoff modeling.