To provide a system and a method for operating an air conditioner using the solar heat even after a vehicle engine is turned off.

The system for operating the air conditioner comprises: an ambient temperature sensor; a cabin temperature sensor; an air conditioner provided with an air inlet part for sucking inside air of a cabin, an air blower for introducing outside air into an inner part of a vehicle and supplying cooled or heated air into the cabin, and a thermoelectric element module for cooling or heating inside the cabin; an air cleaner; a seat cooling/heating module for regulating vehicle seat temperature; a solar cell module providing driving power from solar heat; and a controller for operating the solar cell module to control the air conditioner, the air cleaner, and the seat cooling/heating module according to a magnitude of solar light when the vehicle engine is turned off.