Rice production in the cold region of Northeast China is highly sensitive to irrigation regimes and inter-annual meteorological variations, but the long-term effects of traditional flood irrigation (TFI) and controlled irrigation (CTI) on rice growth, yield formation, water-nitrogen use efficiency, and grain quality remain insufficiently quantified. This knowledge gap hinders the development of sustainable irrigation strategies for improving yield stability and resource use efficiency in the region. To address this, a five-year field experiment (2018–2022) combined with the previously developed ORYZA-N model was conducted to evaluate TFI and CTI in the cold region of Northeast China. Meteorological data (temperature, radiation, rainfall, etc.), rice growth and yield-related traits, water-nitrogen use efficiency, and grain quality were monitored throughout the growing seasons. Key results indicated that July and August were critical for rice spike blooming, grain filling and ripening, as these stages determined final yield by governing sink capacity, grain filling rate and thousand-grain weight (TGW). Inter-annual yield variability was mainly driven by uneven temperature and radiation distribution during the growing season, while excessive rainfall in the reproductive stage of wet years further reduced yields. Water excess or deficit in paddies adversely affected rice growth and yield across all years, emphasizing the need for shallow flood irrigation with timely field drying to stabilize yield. In terms of water-nitrogen use, CTI enhanced water and nitrogen use in wet years, whereas TFI performed better in normal years. For yield, CTI increased effective spikes and yield in wet years (with minimal differences in grain filling rate and TGW between regimes), while TFI produced more spikes and grains to achieve higher yield in normal years. Importantly, CTI did not compromise grain quality compared to TFI. These findings indicate that CTI is a promising strategy for wet years in Northeast China’s cold region, as it improves yield stability and water-nitrogen use efficiency without sacrificing grain quality, while TFI remains suitable for normal years. This study provides a scientific basis for optimizing irrigation management and promoting sustainable rice production in cold regions with variable meteorology.