Tracking the hydrogen and oxygen isotopic compositions of water samples can aid in understanding the water cycle. Compared to that of fresh water, analyzing the hydrogen and oxygen isotopic composition of high-salinity water is still a challenging task owing to the influence of dissolved salts. In this study, desalination was achieved by vacuum extraction, and the oxygen and hydrogen isotope ratios (δ18O and δ2H) were measured using cavity ring-down spectroscopy (CRDS). Different solutions of the individual salts (NaCl, KCl, MgCl2, and CaCl2) were prepared with deionized water (DI) having a known stable isotopic composition. After vacuum extraction, the maximum differences in isotopic composition was no more than 0.09‰ for δ18O and 0.30‰ for δ2H at 4 mol/L NaCl and KCl and 1 mol/L MgCl2 and CaCl2. The isotopic compositions of two high-salinity samples (IAPSO standard seawater and brine water) were determined by the proposed procedure as well as thermal conversion/elemental analyzer-isotope ratio mass spectrometry for comparison. The δ18O and δ2H results obtained using the two methods were consistent. The influence of isotope-salts was completely overcome by the proposed vacuum extraction desalination procedure. Thus, the method enables the rapid extraction of a large number of samples, regardless of the type and origin of the salt solutions, provided the concentrations of MgCl2 and CaCl2 are below 1.0 mol/L.