Many countries are operating a heatwave warning system (HWWS) to mitigate the impact of heatwaves on human health. The level of heatwave warning is normally determined by using the threshold temperature of heat-related morbidity or mortality. However, morbidity and mortality threshold temperatures have not been used together to account for the severity of health impacts. In this study, we developed a heatwave warning system with two different warning levels: Level-1 and Level-2, by analyzing the severity and likelihood of heat-related morbidity and mortality using the generalized additive model. The study particularly focuses on the cases in Seoul, South Korea, between 2011 and 2018. The study found that the threshold temperature for heat-related morbidity and mortality are 30 °C and 33 °C, respectively. Approximately 73.1% of heat-related patients visited hospitals when temperature was between 30 °C and 33 °C. We validated the developed HWWS by using both the threshold temperatures of morbidity and mortality. The area under curves (AUCs) of the proposed model were 0.74 and 0.86 at Level-1 and Level-2, respectively. On the other hand, the AUCs of the model using only the mortality threshold were 0.60 and 0.86 at Level-1 and Level-2, respectively. The AUCs of the model using only the morbidity threshold were 0.73 and 0.78 at Level-1 and Level-2, respectively. The results suggest that the updated HWWS can help to reduce the impact of heatwaves, particularly on vulnerable groups, by providing the customized information. This also indicates that the HWWS could effectively mitigate the risk of morbidity and mortality.