Mitigating air pollutants such as SOx and PM emitted from ships is an important task for marine environmental protection and improving air quality. To address this, exhaust gas after-treatment devices have been introduced, but treating pollutants like SOx and PM individually poses challenges due to spatial constraints on ships. Consequently, a Total Gas Cleaning System (TGCS) capable of simultaneously reducing sulfur oxides and particulate matter has been developed. The TGCS combines a cyclone dust collector and a wet scrubber system. The cyclone dust collector is designed to maintain a certain distance from the bottom of the wet scrubber, allowing exhaust gases entering from the bottom to rise as sulfur oxides are adsorbed. Additionally, the exhaust gases descending through the space between the cyclone dust collector and the wet scrubber collide with the scrubbing solution before entering the bottom of the wet scrubber, facilitating the absorption of SOx. In this study, the efficiency of the developed TGCS was evaluated, and the reduction effects based on design parameters were investigated. Furthermore, the impact of this device on ship engines was analyzed to assess its practical applicability. Experimental results showed that increasing the volume flow rate of the cleaning solution enhanced the PM reduction effect. Particularly, when the height of the Pall ring was 1000 mm and the volume flow rate was 35 L/min, the sulfur oxide reduction effect met the standards for Sulfur Emission Control Areas (SECA). Based on these findings, suggestions for effectively controlling atmospheric pollutants from ships were made, with the expectation of contributing to the development of systems combining various after-treatment devices.