Swift changes in both industrialization and pollution control in China over the past 15 years have created a complex and evolving relationship between emission sources and the depositional sinks of air pollutants. Here, by combining an emissions inventory, an air quality model and a statistical model to estimate bulk deposition (wet plus a part of dry), we present the changes and driving factors of source–sink relationships of typical pollutants throughout China between 2005 and 2020. We find that the deposition of sulfate and nitrate has declined more slowly than the emissions of their precursors, sulfur dioxide and nitrogen oxides, which we attribute, in part, to increased precipitation. In four developed regions of China, enhanced air pollution transport also plays an important role in the slower decline of deposition compared with that of emissions, as has a changing aerosol chemistry in the case of sulfur compounds. Our analysis shows that reducing deposition is not as simple as merely reducing its precursor emissions and suggests that the design of future policies to reduce associated risks may need to vary by region and species, accounting for their evolving interactions over time.