This study aimed to assess the heat-related risk (excess mortality rate) at six cities, namely, Seoul, Incheon, Daejeon, Gwangju, Daegu, and Busan, in South Korea using the daily maximum perceived temperature (PTmax), which is a physiology-based thermal comfort index, the wet-bulb globe temperature, which is meteorology-based thermal comfort index, and air temperature. Particularly, the applicability of PTmax was evaluated using excess mortality rate modeling. An event-based heat-related risk assessment model was employed for modeling the excess mortality rate. The performances of excess mortality rate models using those variables were evaluated for two data sets that were used (training data, 2000–2016) and not used (test data, 2017–2018) for the construction of the assessment models. Additionally, the excess mortality rate was separately modeled depending on regions and ages. PTmax is a good temperature indicator that can be used to model the excess mortality rate in South Korea. The application of PTmax in modeling the total mortality rate yields the best performances for the test data set, particularly for young people. From a forecasting perspective, PTmax is the most appropriate temperature indicator for assessing the heat-related excess mortality rate in South Korea.