This study had two aims: 1) based on a performance evaluation, to set the optimal operating range for a high-concentration ozone generator recently developed with domestic technology; 2) to establish a model-based control strategy to achieve the removal of target compounds. To determine the optimal operating range of the ozone generator, this study considered the energy consumption and oxygen cost per unit ozone generation, as these factors have the greatest influence on the operating cost. This method was in accordance with the methods proposed by the American Ozone Association and the US Environmental Protection Agency. The optimal operating range of the ozone generator was found to be approximately 2 to 14%. Within this range, the total operating cost is minimized, as determined by comparing the generated ozone concentration, oxygen cost, and power consumption. An operation of below 12% capacity may increase the cost of ozone production. Based on the performance evaluation curve, the ozone concentration required to reach the target substance removal rate of 80% can be calculated according to the change in water quality and flow rate of the ozone treatment facility at the wastewater treatment plant and by applying an ozone kinetic model. This method can be used to estimate the per unit production cost. For example, the average total ozone generated and unit production cost required to remove 80% of the group 4 compound iopromide were determined to be at least 17% greater than those required to remove the same amount of sulfamethazine, a group 1 compound. This study proposes a practical control strategy and evaluation method for calculating the operating cost of the ozone generator needed to achieve the target removal rate for categorized target substances.