To realize the trans-scale and high-precision measurement of microstructures, as well as to perform multiple geometrical parameter characterizations of some high-aspect-ratio structures, a nano coordinate measurement system was developed based on a nano measurement machine and a micro tactile probe. The mechanical, electrical, and software interfaces between the probe and positioning platform were designed. After the integration of the probe and positioning platform, the measurement system was calibrated using a standard micro ball. To ensure traceability of the measurement results, the laser sources of three interferometers in the positioning platform were also calibrated using the laser beat frequency. Finally, ultra-high steps with heights of 10 μm and 2 mm and the sidewall angle of a silicon arm were measured using the developed system. The experiments indicated that the system can accurately measure large-size structures and complex MEMS devices.