Significance Atmospheric ammonia plays important roles in fine particle pollution, acid rain, and nitrogen deposition. China, known as the world’s top emitter of gaseous ammonia, plans to control ammonia emissions to mitigate the haze pollution that has recently emerged. However, the complex side effects are still unclear. By integrating a chemical transport model, nationwide measurements, and a sophisticated ammonia emission model, we find that ammonia emission control would significantly aggravate acid rain pollution, thereby offsetting the benefit from reduced fine particle pollution and nitrogen deposition. Our work suggests that region-specific ammonia-control strategies provide a more rational and effective way to achieve the dual benefits of protecting human and ecosystem health in China.