EMER on a thermostat stands for "Emergency Heat" mode. It is a backup system for heating emergencies when the primary heating system fails. Thermostats that have an EM Heat or Aux Heat setting usually rely on a heat pump for the primary heating of the home. When temperatures drop, the air becomes too cold for the heat pump to be an effective method of heating the home. At this point, the secondary heat source, like a gas furnace or electric heat strip, is activated to provide heat to the home. However, when the EM Heat mode is activated, the heat pump is essentially turned off, and only the secondary heating system can provide heat to the home, resulting in higher bills and less efficient heating because you are now relying solely on the secondary system. Therefore, EM Heat should only be used in emergencies.