Trioctylphosphonium triflate, trioctylammonium triflate, triphenylphosphonium triflate and triphenylammonium triflate were synthesized and characterized. It was found that phosphonium-based protic ionic liquids (PILs) exhibit higher thermal stability and ionic conductivity than the corresponding ammonium-based PILs, no matter whether the P and N center atoms are bonded to the electron-donating octyl groups or the electron-withdrawing phenyl groups. The ion conduction behavior of the PILs can be adequately described by the Vogel–Fulcher–Tamman (VFT) equation. The higher ionic conductivity of phosphonium-based PILs may be attributed to their weaker hydrogen bond and Coulombic interactions as well as higher carrier ion concentrations, indicated by infrared analysis, lattice potential energy estimation and VFT fitting results. Interestingly, the stronger hydrogen bonds inside trioctylammonium triflate may lead to a much decreased melting point. Furthermore, compared with electron-withdrawing phenyl, electron-donating octyl enhanced the thermal stability of the PILs.