The purification of indoor pathogenic microorganisms has become a topic of concern. The use of nonwoven media air filters causes high resistance, and the problem of noise limited their application under high air volume. Thus, we propose a micro-electrostatic filter, which has improved performance compared to an electrostatic filter, with a new type of cylindrical structure to tackle indoor pathogenic microbial aerosol pollution. Through simulation, it is found that the filtration performance of a cylindrical structure is better than that of a plate structure under all simulation conditions. For particles larger than 1 μm, the shortest theoretical length of the dust collecting plate required for the cylindrical structure is 34% shorter than that for the plate structure. For 0.1 μm particles, the filtration efficiency of the cylindrical structure is nearly 20~30% (the maximum value is 29.76%) higher than that of the plate structure, while the air velocity is 1.5 m/s~2.5 m/s. The resistance of the cylindrical micro-electrostatic filter is only half of that of the combined plate type micro-electrostatic filter, indicating that the cartridge structure has enormous energy-saving potential. The introduction of the quality factor further proves that the integrated filtration performance of the cartridge micro-electrostatic filter is better. The application of cylindrical micro-electrostatic filters in HVAC systems can help improve indoor air quality and reduce health risks.