A multistage control system of a Positive Temperature Coefficient (PTC) heater for a vehicle is disclosed with a PTC heater that contains heating elements relevant to a first, second, and third stages. An Electronic Control Unit (ECU) outputs a control signal to a first relay, which switches the first stage into an ON and OFF state, for controlling the operation of the first stage of the PTC heater. A heater controller outputs control signals to a second relay and third relay, respectively, for controlling the operation of the second and third stages of the PTC heater, only if the first stage of the PTC heater is in activation via the ECU, wherein the second relay and the third relay each switch the second and third stages into an ON and OFF state.