The mechanism of leaching chalcopyrite by Acidithiobacillus ferrooxidans (A. ferrooxidans) in agar-simulated extracellular polymeric substances (EPS) media was investigated. The results indicate that bacterial EPS can release H~+ and concentrate Fe~(3+); Fe~(2+) is movable between agar-simulated EPS phase and bulk solution phase, but it is difficult for Fe~(3+) to move due to its hydroxylation and EPS complex action; A. ferrooxidans first prefer Fe~(2+) as energy to metabolize compared with chalcopyrite, and a suitable simulated EPS environment for bacterial living is at about pH 1.8; the iron precipitates and jarosites formed by a lot of biologically oxidized Fe~(3+) cover the simulated EPS easily and form an impermeable deposit acting as a limited barrier of ion transport that attenuates the aggressiveness of the bioleaching attack. The EPS layer blocked by iron precipitates or jarosites is responsible for the chalcopyrite passivation.