Ultra-high-efficiency filter media ensure high air cleanliness but need periodic replacement due to pressure drop increase. Adding a pre-filter can extend the filtration system’s service lifetime, yet the pre-filter and main-filter matching lacks systematic study. This research explored how different filter media combinations affected a two-stage ultra-high-efficiency filtration system’s performance. This study focused on five pre-filter grades (F7–F9, H10, H11) and two different types of main-filter media, fiberglass and composite. It was found that the F8 pre-filter media had the best effect on extending the service lifetime of BX and BX + PTFE. The service lifetimes were extended from 44 min and 70 min to 231 min and 326 min, respectively, reaching 5.25 times and 4.65 times the original lifetime. Moreover, the optimal pre-filter grade was less affected by the initial resistance of the main filter. Meanwhile, the BX + PTFE filtration system always showed a longer service lifetime and dust holding capacity compared to the BX filtration system. This study provides guidance for the design and combination of two-stage filters in the context of high-cleanliness applications as well as the improvement of multi-stage filter performance in building ventilation.