Recently, expanded polytetrafluoroethylene (ePTFE) nanofibrous membranes have received extensive attention in the treatment of fine particulate matter (PM2.5). But until now, the influence of membrane structure on the PM2.5 filtration process is still under-investigated. And the application of ultra-thin ePTFE nanofibrous membrane in the treatment of PM2.5 of medium-high concentration has received little report yet. Therefore, three kinds of ultra-thin ePTFE nanofibrous membranes with particle/membrane size ratio (dP/dm) ranging from 0.86 to 4.46 and membrane thickness ≤1 μm were chosen to examine the PM2.5 filtration performance at medium to high concentration (200~1000 mg/m3). All the three membranes showed high PM2.5 filtration efficiencies (>99.5%) and low initial pressure drop (30~130 Pa) benefit from the ultra-thin few-layered crosslinked-network-like structures. In addition, the surfaces of ePTFE menbranes were smooth with roughness commonly less than 1 μm, which reduced the adhesion of the cake layer and hence made it prone to fall off. As a result, the membrane exhibited good regeneration performance in a 4-cycle regeneration experiment. From the comparison of the three nanofibrous ePTFE membranes, it showed the one with the lowest dP/dm ratio (0.86) provided the lowest filtration pressure drop (30 Pa) as well as excellent filtration efficiency (99.93%) and good regeneration performance. But further increasing the membrane pore size may lead to more serious pore-plugging and lower filtration efficiency which had fatal impacts on the PM2.5 filtration performance. In summary, the ultra-thin ePTFE nanofibrous membrane exhibited superior comprehensive performance in filtration of PM2.5 at medium to high concentration which showed a broad application prospects in air purification.