Many errors including perpendicular error influence the accuracy of simulation turntable, which is a crucial equipment in hardware-in-the-loop simulation system. The aim of this paper is to propose a new method of perpendicular error motion separation of rotating spindle on a simulation turntable. Based on transformation matrix and small angle approximation, gesture transformation matrix with various error items is achieved. As a result of this analysis, perpendicular error analysis is carried out when this measurement result is applied to a simulation turntable. Furthermore, this study also permits the user to know how to minimize some error sources of the simulation turntable.