Coal-fired industrial boilers (CFIBs) are an important emission source of mercury. In this study, the mercury flow of the CFIBs in China, including mercury input and output (atmospheric mercury and mercury-containing wastes), was assessed. Besides, the mercury output inventory of wastes (ashes and desulfurization products) from the Chinese CFIBs in 2015 was established for the first time based on the established activity database and updated mercury removal efficiencies. The total mercury inputs of Chinese CFIBs in 2015 were estimated to be 148.4 t, of which the boilers with a capacity of 10 t/h or below were the dominant source, with a total contribution of 41.6%. The atmospheric mercury emissions of CFIBs were 80.7 t, while the total mercury entering wastes including ashes and desulfurization products were 67.77 t. Among them, the mercury in ashes accounted for 80.8% of the mercury in wastes in the country. Provinces with high atmospheric mercury emission intensity (> 3000 g/km2 and > 100 mg/cap) were primarily concentrated in North China, Northeast China, and Northwest China with high heating demands in winter. Significant reductions of mercury emissions were achieved under four scenarios from 2015 to 2030, where the mercury emissions decreased by 75.4–84.6%. However, the reduction potential of mercury emissions narrowed from 2025 to 2030, with an average annual decline of 3.3–6.0%. Besides, based on the energy policies and environmental control measures, three mercury emission reduction paths were proposed for the stages of 2015–2025 and 2025–2030. The uncertainties of mercury inputs, atmospheric mercury emissions, and mercury in wastes of the CFIBs in China in 2015 were estimated at the ranges of − 18.2%– + 20.8%, − 25.1%– + 29.7%, and − 40.7%– + 48.8%, respectively.