A dual type air conditioning control system of a vehicle has a front-seat air conditioner for air-conditioning of a front-seat space and a rear-seat air conditioner for air-conditioning of a rear-seat space of the vehicle. The system includes a front-seat controller configured to control an operation and an output of the front-seat air conditioner, and to calculate a control target value for controlling an output of the rear-seat conditioner. The rear-seat controller is configured to receive the calculated control target value transmitted from the front-seat controller and to control the output of the rear-seat air conditioner based on the transmitted control target value.