High-speed urban development has brought about an increase in per capita income in low- and middle-income countries (LMICs) as well as the high prevalence rate of chronic diseases. Based on a study of chronic diseases from 2011 to 2021 in southeastern China, we used multivariate adjusted logistic regression method to analyze the effect of urban living on the incidence of typical chronic diseases and the trend of such effect with the improvement of public healthcare system. We adopted potential mediating risk factors of urban lifestyles including body mass index (BMI), frequency of dining out, sedentary time, and psychological distress in the adjusted estimation. Baseline results indicate a positive relationship between living in urban areas and the prevalence of type 2 diabetes, hyperlipidemia, and hypertension. Regarding the mediating factors, psychological distress had the highest positive coefficient (Cr) on type 2 diabetes, hyperlipidemia, and hypertension (Cr: 0.4881-0.7084), followed by BMI (Cr: 0.1042-0.1617) and frequency of dining out (Cr: 0.0311-0.0478), and finally, sedentary time (Cr: 0.0103-0.0147). However, regression results on the follow-up survey reveal that trend in the impact of living in urban areas on chronic disease diminished as the level of the healthcare system improved. Additionally, urban living was more positively correlated with the incidence of metabolic disease than with the incidence of cardiovascular disease and cancer. Our findings provide empirical evidence that future urban health planning in LMICs should pay sustained attention to upgrading the level of public health infrastructure covering urban residents as well as rural-to-urban migrants, constructing a long-term dynamic system of chronic disease prevention and control, and regularly monitoring the mental health problems of residents in order to interrupt the process of urban chronic disease prevalence in an early stage.