<p>Soils represent the largest contributor to global nitrous oxide (N₂O) emissions. However, current research efforts predominantly focus on N₂O emissions from agricultural soils, while studies on N₂O emissions from natural soils, another significant source, remain limited. In this study, we explored the magnitude, spatiotemporal dynamics, and drivers of N₂O emissions from China’s natural soils over the period 1980–2022 via machine learning and a compiled novel dataset of 319 field observations. Our results revealed that the N₂O flux per unit area was generally higher in the southeast compared to the northwest, and higher in forests than in grasslands. This spatial and biome heterogeneity was strongly regulated by local hydrothermal conditions and nitrogen availability. The averaged N₂O emissions over the study period were 646.2±27 Gg N₂O yr⁻¹, with approximately equivalent contributions from forests and grasslands. Moreover, there exhibited a significant and increasing trend from 1980 to 2022, with a rate of 2.7 Gg N₂O yr⁻². Such an increase was primarily driven by the expansion of forested area and elevated nitrogen deposition. Our data driven study presents a long term and gridded estimate of N₂O emissions from China’s natural soils, emphasizing the need for future research on changes of greenhouse gas emissions induced by land use change and nitrogen deposition.</p>