In this study, a series of low dielectric constant and transmission loss of polyimide (PI)/organically modified hollow silica nanofiber (m-HSNF) nanocomposites were synthesized via two-step polymerization. Two different PIs were fabricated using two types of diamine monomers with or without fluorine-containing groups and biphenylene structure of dianhydride. The chemical structure and morphology of the fabricated composites were characterized using Nuclear magnetic resonance (NMR), Fourier transform infrared (FTIR) and field-emission scanning electron microscopy (FESEM). The two-step polymerization process successfully manufactured and converted from polyamic acid to polyimide after thermal imidization was proved by the NMR and FTIR results. The FESEM and their related energy-dispersive X-ray spectroscopy (EDS) images of nanocomposites indicate that the m-HSNF is extremely dispersed into the polyimide matrix. The high-frequency dielectric constants of the nanocomposite materials decrease as the presence of fluorine-containing groups in diamine monomers and the loadings of the m-HSNF increase. These findings are probably attributed to the presence of the steric hindrance effect brought by trifluoromethyl groups, and the m-HSNF can disrupt the chain packing and increase the free volume, thus reducing the dielectric properties of polyimides. The transmission loss and its related uncertainty of fabricated composite materials contain excellent performance, suggesting that the fabricated materials could be used as substrate materials for 5G printed circuit board.