This study reports a systematic investigation of electrolytes based on new salts consisting of various cations and the bis(oxalate)borate (BOB) anion for use in electrical double layer capacitors. The quaternary ammonium salts—tetraethylammonium tetrafluoroborate (TEABF4), spiro-(1,1ʹ)-bipyrrolidinium tetrafluoroborate (SBPBF4), 1,1-dimethylpyrrolidinium tetrafluoroborate (DMPBF4), tetraethylammonium bis(oxalato)borate (TEABOB), spiro-(1,1ʹ)-bipyrrolidinium bis(oxalato)borate (SBPBOB), and 1,1-dimethylpyrrolidinium bis(oxalato)borate (DMPBOB)—were successfully prepared in high purity and dissolved in acetonitrile (ACN) at a concentration of 1.0 M. The successful synthesis of the salts was confirmed by nuclear magnetic resonance, ultraviolet–visible, and Fourier-transform infrared spectroscopies. The physicochemical properties and electrochemical performance of the prepared electrolytes, namely, thermal stability, ionic conductivity, viscosity, electrochemical stability window, specific capacitance, and durability, were investigated. Compared to the BF4-containing electrolytes, the new electrolytes based on the BOB anion, particularly the DMPBOB salt, showed dramatically enhanced high-voltage performance at elevated temperature. Electrical double layer capacitors based on 1 M DMPBOB in ACN exhibited a capacitance retention of 55.9% and a coulombic efficiency of >99% after 2000 cycles at a working voltage of 4.0 V and 45 °C. Moreover, X-ray photoelectron spectroscopy suggested that a highly stable protective layer induced by the BOB-containing electrolyte was formed on the negative electrode of the capacitor, inhibiting acute electrolyte decomposition during the cycling test.