Carbon dioxide (CO2) evasion from inland waters is an important component of the global carbon cycle. However, it remains unknown how global change affects CO2 emissions over longer time scales. Here, we present seasonal and annual fluxes of CO2 emissions from streams, rivers, lakes, and reservoirs throughout China and quantify their changes over the past three decades. We found that the CO2 emissions declined from 138 ± 31 Tg C yr−1 in the 1980s to 98 ± 19 Tg C yr−1 in the 2010s. Our results suggest that this unexpected decrease was driven by a combination of environmental alterations, including massive conversion of free-flowing rivers to reservoirs and widespread implementation of reforestation programs. Meanwhile, we found increasing CO2 emissions from the Tibetan Plateau inland waters, likely attributable to increased terrestrial deliveries of organic carbon and expanded surface area due to climate change. We suggest that the CO2 emissions from Chinese inland waters have greatly offset the terrestrial carbon sink and are therefore a key component of China’s carbon budget.