Varietal selection is a critical intrinsic driver for optimizing nitrogen (N) use efficiency and mitigating environmental risks in paddy ecosystems. However, the integrated impacts of varietal disparities on multi-pathway N losses and yield responses have not been systematically quantified on a global scale. We conducted a comprehensive meta-analysis of 96 peer-reviewed publications (encompassing 1651 field observations) to evaluate the distinct patterns in grain yield, N use efficiency (NUE), and gaseous N losses (N2O and NH3) among hybrid rice, conventional indica and japonica rice, and varieties categorized by high vs. low N efficiency. Our results indicate that hybrid rice increased grain yield by approximately 14% and 24% compared to conventional indica and japonica rice, respectively, while simultaneously enhancing NUE by 24% and 7%. Under equivalent N application rates, hybrid rice exhibited significantly lower cumulative N2O emissions than conventional japonica rice, whereas NH3 volatilization was predominantly modulated by fertilization practices and soil physicochemical properties. Aboveground biomass showed a strong positive correlation with plant N uptake (R2=0.67), which was inversely correlated with gaseous N loss fluxes. Subgroup analysis demonstrated that under moderate N input (150–250 kg/hm2), hybrid and high-NUE varieties were most effective in achieving synergistic gains in yield and NUE, particularly in soils characterized by high organic carbon (>12.5 g/kg) and clay-dominant texture (>30% clay). In conclusion, integrating genetic improvements—specifically selecting varieties with high yield potential and superior N efficiency—with optimized agronomic management and soil organic matter enhancement provides a pivotal pathway for achieving the triple-win of reduced N input, stabilized yield, and minimized environmental emissions in global rice production systems.