The invention discloses a method and system for controlling a changeable nozzle pressurizer. The method includes: acquiring a given pressurizing pressure value according to a calculated pressurizing pressure demand value and a calculated pressurizing pressure limit value; performing PID calculation according to a difference between the given pressurizing pressure value and an actual measured pressurizing pressure value so as to acquire a nozzle ring position demand value of the changeable nozzle pressurizer; adding the nozzle ring position demand value and a pressurizing feed forward value to acquire a nozzle ring initial position given value; acquiring a nozzle ring position maximum value from an altitude associated basic pulse chart matching an altitude of a place where an engine is located according to the rotation speed and the torque of the engine; and using the nozzle ring position maximum value to perform limiting value treatment on the nozzle ring initial position given value so as to acquire a nozzle ring position given value, wherein the nozzle ring position given value is used for controlling a position of a nozzle ring of the changeable nozzle pressurizer. The method and the system can effectively control response of the changeable nozzle pressurizer, and then overspeed risk can be avoided when the intake resistance or the pressurizing pressure is increased.