Provided are a seat temperature control system and a control method thereof comprising a sensor unit collecting integrated information including vehicle information on vehicle environment, seat information on a state of a seat, and occupant information on a state of an occupant; an air conditioning device regulating airflow volume and temperature of an indoor space or a seat of the vehicle; and a control unit having a prioritizing criterion on the priority among a plurality of pieces of integrated information, prioritizing the plurality of pieces of integrated information according to the prioritizing criterion, setting target temperature of the output from the seat or the air conditioning device according to the plurality of prioritized pieces of integrated information, and controlling the air conditioning device in order for the temperature of the output from the seat or the air conditioning device to reach the target temperature.