Provided are a magnetic bearing compressor, an air conditioner and a protective air gap value setting method. The magnetic bearing compressor includes: a rotor, a magnetic bearing, a sensor, and a control device. The magnetic bearing is sleeved on the rotor; the sensor is arranged on the magnetic bearing and is configured to detect a distance value between the rotor and the sensor on a preset plane; the control device is configured to receive the distance value and determine the minimum distance value and the maximum distance value between the rotor and the magnetic bearing according to the distance value, and obtain an absolute value of a difference of the maximum distance value and the minimum distance value; and the control device obtains a protective air gap value according to the absolute value and a preset protection coefficient when the absolute value is less than or equal to a preset air gap value.