Evaluating the influence of geometric errors in rotary axes is a common method used by a five-axis machine tool for improving the machining accuracy. In conventional geometric error models, the table coordinate system is considered as the final workpiece coordinate system. In this study, an additional workpiece coordinate transformation was proposed to identify the influence of geometric error. First, a cubic machining test was conducted. Second, the necessity of workpiece coordinate transformation was analyzed, and a method for coordinate transformation was proposed. In addition, both machining simulation and an actual machining experiment of the cubic machining test were conducted to verify the efficiency of the proposed method. The results indicate that the workpiece coordinate transformation is an essential part of the geometric error model for accurately simulating the geometric error influence. The method for identifying the geometric error influence considering the workpiece coordinate transformation is applicable in manufacturing.