Abstract: In order to establish a more accurately and rapid method for hydrogen and oxygen isotopes analysis of water sample, two commercially available equipments of elemental analyzer isotope ratio mass spectrometer (Flash HT-IRMS) and sample preparation device-stable isotope mass spectrometer (GasBench II-IRMS) with the reduction of H₂O samples by reaction with glassy carbon at high temperatures and aqua equilibration techniques, respectively, were used for the analysis of hydrogen and oxygen isotopes of water samples from different sources. The stable isotope measurements results show that both of analytical systems are able to provide good analytical data in accuracy with precision of superior to 0.5‰ (δD) and 0.1‰ (δ¹⁸O), respectively. The comparison of the analytical data from the two analytical systems indicates that Flash HT-IRMS continuous flow method provides better hydrogen and oxygen isotope composition data in reproducibility and accuracy than the data from the other method. In addition, Flash HT-IRMS analysis system can on line simultaneous determination of δD and δ¹⁸O in water samples with short analysis time and sample consumption, only 0.1 μL. Therefore, for the analysis of hydrogen and oxygen isotopes in micro-amounts of water samples, the Flash HT-IRMS analysis system has more advantages.