BackgroundFamine is a risk factor for non-communicable chronic diseases (NCDs), which account for over 80% of deaths in China. The effect of famine on the prevalence of NCDs in terms of various age groups, time periods and cohorts is currently poorly understood.ObjectiveThis study aims to explore long-term trends in the impact of China’s Great Famine (1959–1961) on NCDs in China.MethodsThis study used data from the 2010–2020 China Family Panel Longitudinal Survey across 25 provinces in China. The subjects were aged 18–85 years, and the total number of subjects was 174,894. The prevalence of NCDs was derived from the China Family Panel Studies database (CFPS). An age-period-cohort (APC) model was used to estimate the age, period and cohort effects of NCDs in 2010–2020 and the effect of famine on the risk of NCDs in terms of cohort effects.ResultsThe prevalence of NCDs increased with age. Additionally, the prevalence did not clearly decrease over the survey period. Regarding the cohort effect, people born in the years adjacent to the famine period had a higher risk of NCDs; additionally, females, those born in rural areas, and those who lived in provinces with severe famine and post-famine had a higher likelihood of NCDs.ConclusionsExperiencing famine at an early age or the experience of famine in a close relative’s generation (births after the onset of famine) are associated with an increased risk of NCDs. Additionally, more severe famine is associated with a higher risk of NCDs.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12889-023-16142-4.