Abstract: Continuous flow Gasbench Ⅱ-IRMS online analytical method and dual-inlet IRMS off-line analytical method were used for hydrogen and oxygen isotope composition analysis in water samples. The comparison of the analytical data from the two analytical systems indicates that Dual-inlet IRMS off-line method provides better hydrogen isotope composition data in reproducibility and accuracy than the data from the other method and the determination precision is superior to 1‰. But for oxygen isotope composition analysis, both analytical methods are able to provide good analytical data in both reproducibility and accuracy with precision of superior to 0.2‰. However, continuous flow Gasbench Ⅱ-IRMS online analytical method is of predominance in oxygen isotope composition analysis, especially in micro-amounts of water sample analysis or in large quantity of water sample analysis.