Chemical oxo-precipitation (COP) is a peroxo-aided process that was successfully applied to remove boron from the solution in the previous report. In this study, three-stage Ca-based COP was introduced to treat boron-contained flue gas desulfurization (FGD) wastewater that came from coal-fired power plants in Taiwan. Operating parameters, including pHi, [H2O2]i/[B]0, and [Ca]i/[B]0 (‘i’ represents the stage number) were optimized to reach the permissible effluent boron concentration of 5 mg/L. The effect of sulfate and magnesium in boric acid solution as the interference ions was preliminary investigated. The presence of sulfate and high magnesium concentration ([Mg]0/[B]0 > 0.5) are negatively affected the deboronation process due to the consumption of calcium and hydrogen peroxide, respectively, to form the unrequired precipitate. The optimum condition was resulting in residual boron concentration of 2.5 mg/L reached under the pH1 = pH2 = 10.5, pH3 = 11.0, [H2O2]1/[B]0:[H2O2]2/[B]0:[H2O2]3/[B]0 = 2:2:2, [Ca]2/[B]0:[Ca]3/[B]0 = 1.5:1. FTIR and RAMAN analysis show that most of the boron was removed via Ca(B(OH)3OOH)2 and CaB(OH)3OOB(OH)3 precipitation at 1st and 2nd stage. However, the predominated formation of metal peroxide, metal carbonate, and metal sulfate at 3rd stage provided different removal mechanism of boron through adsorption and co-precipitation. It can be concluded that Multi-stage Ca-based COP has a big potential to be applied to treat boron-contained industrial wastewater, but the re-adjustment is needed due to the varying concentration of wastewater components.