In order to eliminate the disposal issues of toxic chemicals in chemical mechanical planarization, a water-based ultra-polishing experiment with alumina abrasives was investigated for silicon wafer based on Box-behnken theory. It was found that the material removal rate (MRR) was sensitive to pH value, more sensitive to the slurry flow rate, and most sensitive to the oxidizer concentration. Under the optimal conditions of oxidizer concentration (0.44%), slurry flow rate (71.86 mL/min), and natural pH (pH: 7), the highest MRR was derived. Finally, a confuse-understanding of pH on material removal was addressed as well. It was pointed out that the increase in pH leads to the initial decrease in MRR, followed by a rapid increase as pH exceeds 11.