The inventory and input/output balance of trace elements in farmland play an important role in risk assessment and soil management, but there is little information about nationwide changes of the input/output balance of trace elements in farmland in China. In the present study, the inventory of trace element inputs to farmland was updated based on the dataset from the literature published during 2006-2015, and changes of the input/output balance were investigated. Compared with 1999-2006, net inputs of Cr, Ni, and Zn increased by 52.9%, 59.7%, and 20.6%, respectively. The increases in fossil fuel derived energy consumption, industrial manufacture, municipal solid waste incineration, and transportation were the predominant contributors to these increases. Net inputs of Cd, Cu, and Hg decreased dramatically by 46.7%, 25.2%, and 50.4%, respectively. The decreases are due to the strict management of feed additives, fertilizers, and emissions of atmospheric pollutants. Net inputs of As and Pb still remained relatively stable. These results demonstrated that better achievements have been gained by administration of air, water and soil in China. Regulation of atmospheric emission for Cr, Ni, and Zn was recommended as atmospheric deposition was the predominant source for increases of Cr, Ni, and Zn inputs to farmland across China.