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Background: A universally applicable approach that provides standard HALE measurements for different regions has yet to be developed because of the difficulties of health information collection. In this study, we developed a natural language processing (NLP) based HALE estimation approach by using individual-level electronic medical records (EMRs), which made it possible to calculate HALE timely in different temporal or spatial granularities., Methods: We performed diagnostic concept extraction and normalisation on 13•99 million EMRs with NLP to estimate the prevalence of 254 diseases in WHO Global Burden of Disease Study (GBD). Then, we calculated HALE in Chongqing, 2017, by using the life table technique and Sullivan's method, and analysed the contribution of diseases to the expected years "lost" due to disability (DLE)., Findings: Our method identified a life expectancy at birth (LE 0 ) of 77•9 years and health-adjusted life expectancy at birth (HALE 0 ) of 71•7 years for the general Chongqing population of 2017. In particular, the male LE 0 and HALE 0 were 76•3 years and 68•9 years, respectively, while the female LE 0 and HALE 0 were 80•0 years and 74•4 years, respectively. Cerebrovascular diseases, cancers, and injuries were the top three deterioration factors, which reduced HALE by 2•67, 2•15, and 1•19 years, respectively., Interpretation: The results demonstrated the feasibility and effectiveness of EMRs-based HALE estimation. Moreover, the method allowed for a potentially transferable framework that facilitated a more convenient comparison of cross-sectional and longitudinal studies on HALE between regions. In summary, this study provided insightful solutions to the global ageing and health problems that the world is facing., Funding: National Key R and D Program of China (2018YFC2000400)., Competing Interests: We know that a conflict can be actual or potential, and full disclosure to the Editor of all relationships is a requisite. All authors confirm that none conflicts of interest exist and there is nothing to disclose., (© 2021 The Authors. Published by Elsevier Ltd.)