Abstract Atmospheric mercury pollution is a severe threat to both environment and human health. For Beijing economy 2012, this paper compiles an exhaustive inventory for direct mercury emissions and performs an input–output analysis for indirect mercury emission connections. It's estimated that Beijing's direct atmospheric mercury emissions were 2.62 tonnes, mainly contributed by combustion of coal and cement production. Most sectors' indirect emission intensities are larger than direct ones, which indicates that there are considerable inter-sector mercury emission flows embodied in intermediate transactions. The economy avoided 5.30 tonnes of mercury emissions via trade, which double its direct emissions. Mercury emissions induced by Beijing's final consumption were 3 times as many as direct emissions and the largest part was due to capital formation. The results indicate that the end-of-pipe accounting couldn't fully capture urban economy's emissions. Our findings also provide insights for mercury emission mitigation from both the local and systematic perspectives. From the local perspective of direct emissions, the economy can adjust its energy structure and develop clean coal combustion technology as well as mercury removal devices. For the systematic perspective associated with indirect emissions, policy should be extended to manage consumption of the trans-boundary energy and resources.