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In recent years, O3 pollution had been worsening in China and became a major challenge for human health. To evaluate the O3 effects on circulatory and respiratory mortality in Harbin, a high latitude city of northeast China, we applied a time-series study from 2014 to 2016. After collecting data and adjusting for the effects of confounders, we built the generalized additive model to assess the associations between O3 and mortality at different lag days. The results showed that an interquartile-range (IQR) increase in O3 concentration corresponded to excess risk (ER) of 2.00% (95%CI: − 0.25–4.30%) for circulatory mortality at lag 0 and 8.02% (95%CI: 4.18–12.01%) for respiratory mortality at lag 2 days in the single-pollutant model. Stratified analysis showed that O3 had a greater effect on females than on males. The effect of O3 exposure on circulatory mortality was stronger during the warm period, while the opposite trend was founded for respiratory mortality. The sensitivity analysis showed that the effects of O3 were relatively independent and the major results were robust. [ABSTRACT FROM AUTHOR]