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In the context of increasingly frequent and severe natural disasters, scientifically measuring and analyzing the efficiency of natural disaster emergency management in China is of great practical significance for enhancing the performance of the emergency management system and promoting its systematic and high-quality development. This study first applies a super-efficiency SBM-DEA model with undesirable outputs to systematically measure the efficiency of China’s natural disaster emergency management system during the period 2019–2023. Subsequently, the Dagum Gini coefficient and Kernel Density estimation are employed to examine regional disparities and dynamic evolution across eastern, central, western, and northeastern China. Finally, the coefficient of variation and spatial econometric models are applied to test the spatial convergence characteristics of emergency management efficiency. The results indicate that: (1) China’s overall disaster emergency management efficiency remains at a relatively low level and exhibits a fluctuating trend characterized by an initial increase followed by a decline. The regional distribution pattern of emergency efficiency is ranked as “Northeast > Central > West > East”. (2) The average annual contributions of intra-regional disparities, inter-regional disparities, and transvariation density to the overall variation in national emergency management efficiency are 27.58%, 39.90%, and 32.53%, respectively, indicating that inter-regional disparities and transvariation density are the dominant sources of systemic differences among regional subsystems. (3) The national distribution of emergency management efficiency displays a bimodal pattern, indicating polarization; however, the secondary peak is relatively flat, suggesting a weakening trend of provincial-level polarization and a gradual narrowing gap with high-efficiency regions. (4) σ-divergence is observed at the national level and in the central region, while both absolute and conditional β-convergence exist to varying degrees at the national level and across all four regions. Nevertheless, the enhancement of natural disaster emergency management efficiency has not yet realized a system-level transition from convergence in growth rates to convergence in efficiency gaps. In addition, economic development, technological progress, urbanization, and industrial structure exert significantly heterogeneous effects on disaster emergency management efficiency across different regions.