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.