The severity of environmental pollution from acid mine drainage (AMD) is increasingly garnering attention. In this study, the effects of hydraulic shear forces (achieved by regulating the shaking table’s rotation speed) on Fe2+ bio-oxidation and Fe3+ hydrolytic mineralization in an acidic 9K medium-FeSO4-Acidithiobacillus ferrooxidans system (simulated AMD) are investigated. Results reveal that a higher shaking speed favors a higher oxidation rate of Fe2+, whereas a very low or high shaking speed restricts the removal of Fe3+. Shaking table rotation speeds of 120–180 rpm were preferred for biomineralization treatment in the simulated AMD. As the initial concentration of Fe2+ in the system decreased from 9.67 to 0 g/L in 40 h, the dissolved O2 (DO) in the solution dropped to its lowest concentration after 20 h and then increased to its initial level between 40 and 120 h. However, the corresponding total Fe (TFe) precipitation efficiency increased with the increasing mineralization time after 40 h. The effect of O2 supply time on biomineralization revealed that DO was mainly used in Fe2+ bio-oxidation. After Fe2+ was completely oxidized by A. ferrooxidans, the precipitation efficiency of TFe was independent of the O2 supply.