In the present invention, a method and a system for controlling a compressor are provided. The method includes the steps of: providing a condenser connected to the compressor, and at least one evaporator connected to the condenser; measuring an inlet pressure and an outlet pressure of the compressor to obtain a flow rate of the condensate; determining a secure flow rate and a demanding flow rate based on a total number of the at least one evaporator; comparing at least two of the flow rate, the demanding flow rate and the secure flow rate with each other to obtain a compared result; and controlling the compressor based on the comparing result.