In a hard disk drive (HDD), the zero crossing points (ZCPs) of back-EMF generated in the spindle motor armature windings are used as rotor position signal for realizing precision motor speed control. The error of ZCP is a major concern, especially for HDDs with ultrahigh data recording densities. In the paper, several causes that induce the ZCP error are analyzed, and these problems are induced during the motor design and production. Both the analytical and numerical methods are used in the analysis to study the influence of the electromagnetic structure on the ZCP. Solutions are then proposed to reduce the errors of the ZCP during the motor design phase.