The purpose of this study is to develop a scrubber wastewater cleaning system to improve the efficiency of odor reduction. We evaluated the changes in scrubber wastewater quality and odor reduction efficiencies before and after applying the pilot system. We determined that it was possible to extend the replacement cycle by two times or more considering the turbidity change and organic removal efficiency. Butyraldehyde, a major odor-causing substances in the exhaust gas of the target facility, is soluble in water. As a result, the odor reduction efficiency was improved by removing the butyraldehyde in the scrubber wastewater. Economically, it is possible to save about 12 million won per year. Thus, it is necessary to keep scrubber wastewater clean in order to improve the deodorization efficiency and reduce the cost of disposal.