Mercury (Hg) exposure poses substantial risks to human health. Investigating a longer chain from economic activities to human health can reveal the sources and critical processes of Hg-related health risks. Thus, we develop a more comprehensive assessment method which is applied to mainland China—the largest global Hg emitter. We present a map of Hg-related health risks in China and estimate that 0.14 points of per-foetus intelligence quotient (IQ) decrements and 7,360 deaths from fatal heart attacks are related to the intake of methylmercury in 2010. This study, for the first time, reveals the significant impacts of interprovincial trade on Hg-related health risks across the whole country. For instance, interprovincial trade induced by final consumption prevents 0.39 × 10⁻² points for per-foetus IQ decrements and 194 deaths from fatal heart attacks. These findings highlight the importance of policy decisions in different stages of economic supply chains to reduce Hg-related health risks.