There is provide a method for controlling a shape measuring apparatus that synchronize an acceleration/deceleration changing timing of a velocity pattern with a control sampling cycle, and prevents a control lag.Based on a shape of a movement path set based on preliminarily-obtained shape data of an object to be measured, a velocity pattern for a probe to move along the movement path.It is determined whether a velocity changing timing of the velocity pattern is synchronized with a control sampling cycle of a shape measuring apparatus.When the velocity changing timing of the velocity pattern is not synchronized with the control sampling cycle, the velocity pattern is corrected such that the velocity changing timing of the velocity pattern is synchronized with the control sampling cycle of the shape measuring apparatus.