This disclosure provides a machine tool adjustment method and system thereof. The machine tool adjustment method includes the following steps: enabling a machine tool to perform a circular test; obtaining a measured error value Em from a measuring instrument, and the measured error value Em is defined by the difference between the actual circular trajectory and the preset circular trajectory during the circular test; determining an error condition of the tool machine from the measured error value Em; determining whether the error condition is less than a predetermined criteria; if not, defining a compensation parameter according to the error condition and enabling the machine tool to perform another circular test according to the set compensation parameter until the error condition is less than the predetermined criteria; and if yes, ending the circular test and the machine tool adjustment is finished.