Atmospheric ammonia has been hazardous to the environment and human health for decades. Current inventories are usually constructed in a bottom-up manner and subject to uncertainties and incapable of reproducing the spatiotemporal characteristics of ammonia emission. Satellite measurements, for example, Infrared Atmospheric Sounder Interferometer (IASI) and Cross-Track Infrared Sounder, which provide global coverage of ammonia distribution, have gained popularity in ammonia emission estimation through data assimilation methods. However, satellite-based emission inversion studies on China are limited. In this study, we propose a four-dimensional ensemble variational-based ammonia emission inversion system to optimize ammonia emissions in China. It was developed by assimilating the IASI ammonia retrievals onboard Meteorological Operational satellite A and B into a chemical transport model Goddard Earth Observing System Chemical model (GEOS-Chem). Monthly inversion experiments were conducted in April, July, and October 2016 to test the performance. The inversion result indicated that the prior inventory from the MEIC model captured ammonia spreads in general; however, it heterogeneously underrated the emission intensity. The increments obtained in the assimilation were as high as 50% in North, East, and Northwest China. The posterior emission inventory presented a regional emission flux consistent with relevant studies. Driven by the optimized source estimate, GEOS-Chem provides superior results than using the prior in the evaluation of the assimilated IASI retrievals and the surface ammonia concentration measured by the ground-based Ammonia Monitoring Network in China.