An apparatus for heat-treating a substrate includes: a stage where the substrate is disposed; a heating part configured to change an output; a first temperature measurement part configured to measure a temperature at which the substrate is heated; a second temperature measurement part configured to measure the temperature, and having a level of measurement accuracy which is lower than that of the first temperature measurement part in a first temperature region and is higher than that of the first temperature measurement part in a second temperature region; a temperature calculator configured to calculate a weighted average temperature of the temperatures measured by the first and second temperature measurement parts if a reference temperature is in a temperature range between the first and second temperatures, and configured to change a weight of the weighted average temperature; and a controller configured to control the output based on the weighted average temperature.