Objective: Few studies have examined the spectrum and trends of non-communicable diseases (NCDs) in inpatients in eastern coastal China, which is transforming from an industrial economy to a service-oriented economy and is the most economically developed region in the country. This study aimed to dynamically elucidate the spectrum and characteristics of severe NCDs in eastern coastal China by analysing patients’ longitudinal electronic health records (EHRs). Setting: To monitor the spectrum of NCDs dynamically, we extracted the EHR data from 12 general tertiary hospitals in eastern coastal China from 2003 to 2014. The rankings of and trends in the proportions of different NCDs presented by inpatients in different gender and age groups were calculated and analysed. Participants: We obtained a total sample of 1,907,484 inpatients with NCDs from 2003 to 2014, 50.05% of whom were male and 81.53% were aged 50 years or older. Results: There was an increase in the number of total NCD inpatients in eastern coastal China from 2003 to 2014. However, the proportion of chronic respiratory diseases and cancer inpatients decreased over the 12-year period. Compared with men, women displayed a significant increase in the proportion of mental and behavioural disorders (P<0.001) over time. Additionally, digestive diseases and sensory organ diseases significantly decreased among men, but not women. The older group accounted for a larger and growing proportion of the NCD inpatients, and the most common conditions in this group were cerebral infarctions, coronary heart disease and hypertension. In addition, the proportion of 21- to 50-year-old inpatients with diabetes, blood diseases or endocrine diseases skyrocketed from 2003 to 2014 (P<0.001). Conclusions: The burden of inpatients' NCDs increased rapidly, particularly among women and younger people. The NCD spectrum observed in eastern coastal China is a good source of evidence for developing prevention guides for regions experiencing transition.