Rice sustains nearly half of the global population, yet its nitrogen (N) use efficiency remains low, undermining both food security and environmental integrity. Rice predominantly absorbs ammonium (NH4 +), which is readily nitrified and lost through irrigation and drainage, posing a persistent management challenge. Integrating 1756 paired field observations and global modelling, we show that using enhanced-efficiency fertilizers to maintain soil NH4 + relative to conventional practices increases rice yield by 6%-10% and N use efficiency by 18%-33%, while reducing ammonia (NH3) volatilization by 16%-50%, nitrous oxide (N2O) emissions by 25%-49%, and methane (CH4) emissions by 9%-30%. This N transformation-based management could reduce global N fertilizer inputs by 1.4 +/- 0.06 million tonnes (Tg), generate an additional 72 +/- 13 Tg of rice, and lower N2O, CH4, and NH3 emissions by 0.07 +/- 0.02, 6.8 +/- 2.0, and 0.6 +/- 0.2 Tg, respectively, equivalent to an annual reduction of about 202 Tg CO2-eq. The total social benefit is valued at US$51 +/- 5 billion, including US$29 +/- 2 billion in added food value, achieved with only US$1.6 +/- 0.6 billion in fertilizer investment and US$0.9 +/- 0.1 billion in transaction costs. Aligning N transformation processes with crop N preference thus represents a pivotal strategy for sustaining rice productivity while minimizing environmental impacts.