The non-repetitive run-out(NRRO) of ball bearing critically influences the rotational accuracy of a machine tool. The quality of manufacturing can be improved by reducing the value of NRRO. This article developed a new ball bearing measuring system to investigate the NRRO caused geometrical errors of the bearing parts include inner and outer races and balls. The characteristic of the proposed measuring system as follows:(1) A high-precision hydrostatic spindle is applied to drive the inner race of the test bearing to obtain the system accuracy; (2) Measurable and variable axial preload is adopted to simulate the operating condition of bearings; (3) A 2 degrees of freedom flexure hinge mechanism (2-DOF FHM) is used to prevent the outer race from rotating; (4) Two capacitive sensors are used to measure radial error of the test bearing to ensure nano resolution.