A bottom-up inventory of atmospheric emissions of five precedent-controlled toxic heavy metals (HMs), including mercury (Hg), arsenic (As), lead (Pb), cadmium (Cd), and chromium (Cr), from primary anthropogenic sources in China is established for the period 2000–2010. Total emissions of HMs demonstrate a gradually ascending trend along with the increase of coal consumption and industrial production, which are estimated at approximately 842.22 t for Hg, 4196.31 t for As, 29272.14 t for Pb, 795.29 t for Cd, and 13715.33 t for Cr for 2010. Coal combustion is found to be the primary source of HMs emissions. Owing to the dramatic differences of coal use by industrial and power sectors among provinces, spatial allocation performs remarkably uneven characteristics, and spatial distribution features are demonstrated by allocating the emissions into 0.5° × 0.5° grid cells with GDP and population as surrogate indexes. Further, HMs emissions from specified anthropogenic sources under three different control scenarios for the target year 2015 are projected, and collaborative and specialized control strategies are proposed to meet the demand of emission reduction goals of different regions. In the future, a whole processes control management system will be the most effective way for control of HMs.