Studies on the pattern of heatwave mortality using nationwide data that include rural areas are limited. This study aimed to assess the risk of heatwave-related mortality and evaluate the health risk-based definition of heatwave. We collected data on daily temperature and mortality from 229 districts in South Korea in 2011–2017. District-specific heatwave-related mortality risks were calculated using a distributed lag model. The estimates were pooled in the total areas and for each urban and rural area using meta-regression. In the total areas, the threshold point of heatwave mortality risk was estimated at the 93rd percentile of temperature, and it was lower in urban areas than in rural areas (92nd percentile vs. 95th percentile). The maximum risk of heatwave-related mortality in the total area was 1.11 (95% CI: 1.01–1.22), and it was slightly greater in rural areas than in the urban areas (RR: 1.23, 95% CI: 0.99–1.53 vs. RR: 1.10, 95% CI: 1.01–1.20). The results differ by age- and cause-specific deaths. In conclusion, the patterns of heatwave-related mortality risk vary by area and sub-population in Korea. Thus, more target-specific heatwave definitions and action plans should be established according to different areas and populations.