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In the midst of the COVID-19 pandemic, new requirements for clean air supply are introduced for heating, ventilation, and air conditioning (HVAC) systems. One way for HVAC systems to efficiently remove airborne viruses is by filtering them. Unlike disposable filters that require repeated purchases of consumables, the electrostatic precipitator (ESP) is an alternative option without the drawback of reduced dust collection efficiency in high-efficiency particulate air (HEPA) filters due to dust buildup. The majority of viruses have a diameter ranging from 0.1 μm to 5 μm. This study proposed a two-stage ESP, which charged airborne viruses and particles via positive electrode ionization wire and collected them on a collecting plate with high voltage. Numerical simulations were conducted and revealed a continuous decrease in collection efficiencies between 0.1 μm and 0.5 μm, followed by a consistent increase from 0.5 μm to 1 μm. For particles larger than 1 μm, collection efficiencies exceeding 90% were easily achieved with the equipment used in this study. Previous studies have demonstrated that the collection efficiency of suspended particles is influenced by both the ESP voltage and turbulent flow at this stage. To improve the collection efficiency of aerosols ranging from 0.1 μm to 1 μm, this study used a multi-objective genetic algorithm (MOGA) in combination with numerical simulations to obtain the optimal parameter combination of ionization voltage and flow speed. The particle collection performance of the ESP was examined under the Japan Electrical Manufacturers’ Association (JEMA) standards and showed consistent collection performance throughout the experiment. Moreover, after its design was optimized, the precipitator collected aerosols ranging from 0.1 μm to 3 μm, demonstrating an efficiency of over 95%. With such high collection efficiency, the proposed ESP can effectively filter airborne particles as efficiently as an N95 respirator, eliminating the need to wear a mask in a building and preventing the spread of droplet infectious diseases such as COVID-19 (0.08 μm–0.16 μm).