An embodiment method for controlling a compressor of a vehicle includes selectively controlling an operation of the compressor by determining and comparing a discharge pressure of the compressor and a temperature of an inverter with predetermined values based on data detected in real time when the compressor is operated to cool or heat an interior of the vehicle and operating a protection mode to prevent thermal burnout of the inverter in response to a determination that the discharge pressure of the compressor is higher than an operation stop pressure.