The denitrifier method is widely used as a novel pretreatment method for the determination of nitrogen and oxygen isotope ratios as it can provide quantitative and high-sensitivity measurements. Nevertheless, the method is limited by relatively low measurement accuracy for δO. In this study, we analyzed the factors influencing the accuracy of δO determination, and then systematically investigated the effects of dissolved oxygen concentrations and nitrate sample sizes on estimates of the δN and δO of nitrate reference materials. The δO contraction ratio was used to represent the relationship between the measured difference and true difference between two reference materials. We obtained the following main results: (1) a gas-liquid ratio of 3:10 (v/v) in ordinary triangular flasks and a shaking speed of 120 r/min produced an optimal range (1.9 to 2.6 mg/L) in the concentration of dissolved oxygen for accurately determining δO, and (2) the δO contraction ratio decreased as nitrate sample size decreased within a certain range (1.0 to 0.1 μmol). Our results suggested that δO contraction is influenced mainly by dissolved oxygen concentrations in pure culture, and provided a model for improving the accuracy of oxygen isotope analysis.