The improvement of ultra-precision machining technology has significantly boosted the demand for the surface quality and surface accuracy of the workpieces to be machined. However, the geometric shapes of workpiece surfaces cannot be adequately manufactured with simple plane, cylindrical, or spherical surfaces because of their different applications in various fields. In this research, a method was proposed to generate tool paths for the machining of complex spherical surfaces based on an ultra-precise five-axis turning and milling machine with a C-Y-Z-X-B structure. Through the proposed tool path generation method, ultra-precise complex spherical surface machining was achieved. First, the complex spherical surface model was modeled and calculated, and then it was combined with the designed model to generate the tool path. Then the tool paths were generated with a numerically controlled (NC) program. Based on an ultra-precision three-coordinate measuring instrument and a white light interferometer, the machining accuracy of a workpiece surface was characterized, and the effectiveness of the provided tool path generation method was verified. The surface roughness of the machined workpiece was less than 90 nm. Furthermore, the surface roughness within the spherical region appeared to be less than 30 nm. The presented tool path generation method in this research produced ultra-precision spherical complex surfaces. The method could be applied to complex spherical surfaces with other characteristics.