Pneumoconiosis in mines occupied more than 90% of the total number of occupational diseases, poses tremendous pressure and challenges on the development of personal protection materials with high dust filtration efficiency and long-lasting comfortable wearing. In this study, a kind of polyethylene terephthalate (PET) based filter media with the bead-on-string structure and hydrophobic/oleophobic property was designed and fabricated by electrospinning technology. Nanoscale silicon dioxide (SiO2NPs) and fluorinated polyurethane (PU) used in this work were benefited for the microstructure, surface energy and hydrophobic/oleophobic property, respectively. The morphology and composition of the membranes were conducted by scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS) and fourier transform infrared spectroscopy (FTIR). Furthermore, the filtration performance, pressure drop, moisture permeability and breathing comfortable performance were measured for the study of personal protection of dust. The results showed that at the air flow of 85 L min−1, PET/SiO2/FPU double-layer nanofibrous membrane showed high filtration efficiency and low pressure drop with the filtration efficiency of 99.96%, pressure drop of 142.5 Pa and quality factor of 0.055 Pa-1, respectively. A long term of 24 h water vapor test had proved that this membrane held an outstanding moisture permeability ability of 5296.325 g (m2 24 h)−1. Compared with the commercial 3701CN filter media, the advantages of the regular breathing frequency and strong heart rate control ability indicated that this PET/SiO2/FPU double-layer membrane had the better wearing comfortable performance with broad application prospects in the personal protection of dust in mines.