We use a two-temperature hydrodynamical formulation to determine the temperature and density structures of the post-shock accretion flows in magnetic cataclysmic variables (mCVs) and calculate the corresponding X-ray spectra. The effects of two-temperature flows are significant for systems with a massive white dwarf and a strong white-dwarf magnetic field. Our calculations show that two-temperature flows predict harder keV spectra than one-temperature flows for the same white-dwarf mass and magnetic field. This result is insensitive to whether the electrons and ions have equal temperature at the shock, but depends on the electron–ion exchange rate, relative to the rate of radiative loss along the flow. White-dwarf masses obtained by fitting the X-ray spectra of mCVs using hydrodynamic models including the two-temperature effects will be lower than those obtained using single-temperature models. The bias is more severe for systems with a massive white dwarf.