To control heavy metal pollution effectively, prevention of heavy metal accumulations in agricultural soils should be the priority rather than remediation of heavy metal contamination. In this research, papers which contained input and output fluxes of Cd, As, Cr, Hg, and Pb in topsoil (the plough layer) of agricultural lands in Hunan, Zhejiang, the Yangtze River Delta, Hainan, and China as a whole were explored. Fluxes of heavy metal species were recalculated, and future trends of pollution were predicted. Also, cases regarding the application of technologies to control the input and output of heavy metals were analyzed. Results indicated that atmospheric decomposition was the dominant input source of heavy metals in all study sites except Hainan. The relative contributions of fertilizers, irrigation water, and straw returning fluctuated greatly among different sites. Cd pollution in all sites was the most serious, followed by Cr and Pb. In Hunan, Cd has already exceeded the maximum limit value and needs to be controlled urgently. The input of heavy metals from irrigation water, fertilizers, and straw returning could be controlled by proposing more policies to manage their quality and application amounts. The amount of heavy metals absorbed by plants could be increased by cultivating crops with hyperaccumulators and high-biomass plants.