The concept of non-repetitive run-out （NRRO） of the precision ball bearing was defined and introduced into the spindle system investigation. The numerical calculation formulas of NRRO caused by the geometric errors of inner and outer rings, and the ball, as well as the ball number variation of the high speed corner contact ball bearing were derived based on the rolling bearing geometry, the elasticity theory and the raceway control theory. A dynamic prediction model was built for the spindle system to consider the effect of NRRO to reveal the impact of NRRO on the precision spindle behavior in the design stage. The calculation examples and the theoretical analysis showed that when only one ball has large error, NRRO reduces with the increase of number of balls in a rolling bearing, the effect of geometric errors in the inner and outer rings on NRRO is small,and the effect of geometric error of the ball surface is significant. On the basis of the proposed prediction model, a design method to restrain NRRO of the spindle system was proposed based on the response surface to overcome theshortcoming in this aspect of the existing deign method, providing a theoretical basis and references for the study of the precision bearing system.