Recent research has investigated spatial variation in temperature-related health risks and regional-level vulnerability. However, although a region has multiple advantages and disadvantages, the intersectionality of these factors has been overlooked. This study assessed spatial variation in heat-mortality associations in South Korea and investigated how regional characteristics intersect and interact to create distinct vulnerability patterns using a novel intersectionality framework. We analyzed the association between heat (defined as daily mean temperature at the 99th percentile) and non-accidental mortality across 229 regions of South Korea during 2011–2020. We conducted two-stage time-series analysis with a distributed lag nonlinear model to investigate heat-mortality associations and their spatial variations at the regional level. We then applied a multilevel analysis of individual heterogeneity and discriminatory accuracy framework to examine the role of intersectional strata in explaining the spatial variation of heat-related risks. Heat-related mortality risks were spatially heterogeneous. The multiply disadvantaged regions (having a low annual mean temperature, a high proportion of older housing stock, and a low proportion of timely emergency room visits) exhibited the highest heat-related relative risk (RR) of 1.105 (95% confidence interval [CI]: 1.097, 1,112), while the multiply advantaged regions exhibited the lowest heat-related RR of 1.065 (95% CI: 1.057, 1.072). These intersectional inequalities are primarily driven by additive effects, with minimal contribution from interaction effects. Our findings suggest the need to develop region-specific heat adaptation strategies that address local vulnerability. Employing an intersectional lens provides a more comprehensive understanding of spatial variation in heat-related health risks.