Geometric error and thermal error of the five-axis CNC machine tool are two important factors that affect the machining accuracy of workpiece. The analysis of these error factors can effectively improve the machining accuracy of thin-walled workpiece. Firstly, based on the homogeneous coordinate transformation method, the geometric error model of rotating axis of five-axis CNC machine tool with double turntable is formulated. Then, on the basis of standard ball, the machine contact measurement is carried out. Twelve geometric errors of the two rotating axles are identified. These errors consider the mutual influence between the two rotating axles and the influence of thermal error. Finally, the geometric error field in the machining space of five-axis CNC machine tool is analyzed. In this machining space, the geometric error gradually increases from the center to the outside. When the rotation angle of axle increases, the maximum error also increases. Compared with other position error identification methods, the measurement accuracy of the proposed method meets the processing requirements. The measurement time only needs 30 min.