To achieve high-precision measurements of these components, micro/nano contact probes and white light interferometric probes must be combined for composite measurement. This paper presents a method to unify the spatial coordinate systems of the two probes using calibration points from a custom calibrator and the unit quaternion method to derive the spatial transformation matrix, evaluated by root mean square error (RMSE). A novel calibrator was designed to offer stable reference points, with a model linking their accuracy to coordinate unification precision. Additionally, a data fusion method blending spatial error ellipsoid search with weighted least squares was proposed, demonstrating a registration accuracy of 1.889 μm. This method decreased the relative error by 16% and improved repeatability precision by 38% compared to traditional least squares. The research enhanced the measurement precision and data fusion stability of composite measurement systems.