Due to the increasing environmental and economic costs associated with nitrogen (N) consumption, improving N use efficiency in rice cultivation systems is of great importance. In this regard, the combined effect of different surface and subsurface drainage systems and water management on the nitrogen harvest index (NHI) of rice was investigated. During three rice growing seasons (2014 to 2016), two rice varieties of Tarom Hashemi and Tarom Daylmani were cultivated under alternate wetting and drying in paddy fields with surface and subsurface drainage systems. At harvest, grain yield and biomass and plant and seed nitrogen were measured. The NHI was determined as the ratio of grain nitrogen to nitrogen absorbed by aboveground part of plant. The amount of NHI was directly related to the amount of urea fertilizer used, varying between 58.31 and 68.45 in different seasons. The average nitrogen absorbed by the Hashemi and Daylmani plants in the subsurface drainage systems was 161.7 and 155.7 kg ha-1, respectively, and in the control was 144.7 and 193.7 kg ha-1, respectively. Also, the average grain yield, grain nitrogen, harvest index and NHI in the subsurface drainage systems were 5329.3 kg ha-1, 105.9 kg ha-1, 37.8% and 67.2%, respectively, and in the control treatment was 4667.7 kg ha-1, 88.6 kg ha-1, 32.4% and 56.3%, respectively. Based on the results, drainage through subsurface drainage systems under intermittent irrigation and drainage management can improve the N use efficiency in rice cropping system