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Geographical inequalities in premature mortality and the role of neighbourhood social determinants of health (SDOH) have been less explored. This study aims to assess the geographical inequalities in premature mortality in Taiwan and how neighbourhood SDOH contribute to them and to examine the place-specific associations between neighbourhood SDOH and premature mortality. We used township-level nationwide data for the years 2015 to 2019, including age-standardized premature mortality rates and three upstream SDOH (ethnicity, education, and income). Space-time scan statistics were used to assess the geographical inequality in premature mortality. A geographical and temporal weighted regression was applied to assess spatial heterogeneity and how neighbourhood SDOH contribute to geographic variation in premature mortality. We found geographical inequality in premature mortality to be clearly clustered around mountainous rural and indigenous areas. The association between neighbourhood SDOH and premature mortality was shown to be area-specific. Ethnicity and education could explain nearly 84% variation in premature mortality. After adjusting for neighbourhood SDOH, only a handful of hotspots for premature mortality remained, mainly consisting of rural and indigenous areas in the central-south region of Taiwan. These findings provide empirical evidence for developing locally tailored public health programs for geographical priority areas.