The measurement method of bearing inner ring radial runout and the installation methods of paired bearings are introduced. By comparing and analyzing the two installation modes of both in the same and opposite directions of radial runout of the paired bearings, it is concluded that when the bearing is installed in the same direction of radial runout, the translation error of axis is increased to reduce the shaking error of the shafting system. So the effect of compensating shafting system error is obtained and the rotation accuracy of the shafting system is improved. After the errors of Class P5 paired bearings are compensated, the maximum shaking error of the shafting system is 2.45 second of arc.