A cutting tool controller and method of controlling are provided. The method includes providing a swing angle for the cutting tool, obtaining a swing vector of the cutting tool through kinematics calculation according to the swing angle, using the swing vector of the cutting tool to calculate a set of possible solutions of a swaying angle of the cutting tool, selecting a possible solution satisfying an operation condition of the machine from the set of possible solutions, using the selected possible solution to calculate an offset of positions of the cutting tool before and after swaying, so as to generate a compensation vector, calculating required compensation values for three axes of the machine according to the compensation vector, and outputting a control command including the compensation values, such that the cutting tool of the machine or a working table for placing the workpiece thereon of the machine moves correspondingly.