A controller and a method for a machine tool, capable of discriminating the factors in overheating, and taking appropriate measures depending on each factor. A first amplifier of the controller has an acceleration/deceleration judging part which judges as to whether the spindle motor is accelerated or decelerated; a first temperature estimating part which estimates a first amount of change in temperature of the spindle motor when the spindle motor is in the acceleration/deceleration state; a second temperature estimating part which estimates a second amount of change in temperature of the spindle motor when the spindle motor is in the steady state; a comparing part which compares the first and second estimated values. A numerical controlling part of the controller transmits an operation command for changing the operation of at least one of the spindle motor and a feed shaft motor, when the spindle motor is overheated.