Northeast China (NEC) has recently become one of the largest commercial rice production regions in China. However, the increased production combined with increasingly frequent climate oscillations is severe competing for fresh water with the non-agricultural sectors in this region and is threatening national food security. In this study, the ORYZA (v3) crop model was used to estimate the rice yields and water applications under three management regimes, continuous flooded irrigation (CF), alternate wetting and drying (AWD), and rain-fed (RF), in the full nutrient supply and biotic-stress-free conditions in NEC from 1961 to 2016. The predicted average rice yields in these three production regimes were 12.7, 12.7 and 10.6 t ha−1. El Niño events reduced yields by 2.5% and 2.4% (P < 0.05) in the CF and AWD regimes, respectively, compared with those in Neutral years. The simulated total water application in the CF, AWD and RF regimes were 1437.3, 706.1 and 523.7 mm, respectively. The total water application decreased 50.9% and 63.6% in the AWD and RF regimes compared with the CF regime, respectively. El Niño events decreased water application by 1.7% and 1.2% in the CF and AWD, respectively (P < 0.05). In addition, the sea surface temperature (SST) impacts on rice yield varied among water management regimes in NEC. El Niño events decreased rice yield under CF and AWD, implying that El Niño may hammer rice production in NEC and impact China’s food security in the future. In addition, AWD management significantly decrease rice water application during both ENSO and non-ENSO years and is a water-saving technology for local government and producers to address the challenge of increasing water application from non-agriculture sectors.