Atmospheric ammonia (NH3) has multiple impacts on the environment, climate change, and human health. China is the largest emitter of NH3 globally, with the dynamic inventory of NH3 emissions remaining uncertain. Here, we use the second national agricultural pollution source censuses, integrated satellite data, 15N isotope source apportionment, and multiple models to better understand those key features of NH3 emissions and its environmental impacts in China. Our results show that the total NH3 emissions were estimated to be 11.2 ± 1.1 million tonnes in 2020, with three emission peaks in April, June, and October, primarily driven by agricultural sources, which contributed 74% of the total emissions. Furthermore, employing a series of quantitative analyses, we estimated the contribution of NH3 emissions to ecosystem impacts. The NH3 emissions have contributed approximately 22% to secondary PM2.5 formation and a 16.6% increase in nitrogen loading of surface waters, while ammonium deposition led to a decrease in soil pH by 0.0032 units and an increase in the terrestrial carbon sink by 44.6 million tonnes in 2020. Reducing agricultural NH3 emissions in China would contribute to the mitigation of air and water pollution challenges, saving damage costs estimated at around 22 billion US dollars due to avoided human and ecosystem health impacts.