BACKGROUND: Although significant progress has been made in the health status of Chinese citizens, disparities are still strikingly evident. This paper reveals the interconnection between social deprivation and the health of the Chinese population using the latest census data, and delves into the impact of social deprivation on health outcomes. METHODS: To assess social deprivation, this study selected 14 indicators from six domains: income, employment, education, housing condition, housing area, and demographic structure. The social deprivation value was calculated using entropy method, variation coefficient method, CRITIC method, and principal component analysis method, and its spatial distribution was compared. Meanwhile, the best models are selected from ordinary least squares regression models, spatial lag models and spatial error models to analyze the effect of social deprivation on health outcomes according to the performances of these models. RESULTS: The spatial distribution of social deprivation in China displays notable heterogeneity. The best models indicates that social deprivation is negatively correlated with mortality rate of Class A and B infectious diseases, average life expectancy and proportion of healthy elderly, but positively correlated with incidence rate of Class A and B infectious diseases, maternal mortality rate, and prevalence rate of low-weight children. The part of regression models for analyzing the relationship between social deprivation and metrics like incidence rate of infectious diseases, maternal mortality rate, average life expectancy, and proportion of healthy elderly are in the form of spatial lag. The part of regression models for analyzing the relationship between social deprivation with mortality rate of Class A and B infectious diseases and prevalence rate of low weight children are in the form of spatial error. CONCLUSION: Social deprivation impacts the health of different populations, and this influence exhibits correlation and interaction across various regions. Therefore, it is necessary for governments to develop policies, particularly those aimed at enhancing the equality of public health services, to address the imbalance in regional development, allocate resources scientifically, and narrow the gap in economic, social, and healthcare development across regions.