The present invention relates to a control method of an air conditioner system for a vehicle. The method of controlling an air conditioning system for a vehicle enables a user to recognize whether economical heating is available, while a vehicle travels. The method includes the steps of: (A) when starting of the vehicle is in an on state, confirming a heating condition and a waste heat source state while the vehicle travels, and predicting power consumption of an electric heater; and (B) comparing a power consumption reference value of the electric heater with a power consumption prediction value of the electric heater, displaying that economical heating is available or unavailable on the display unit, determining whether to turn off the starting of the vehicle, and terminating a control.