Position sensing is essential to testify the validity of the mechanical design and verify the performance in micromanipulation. A practical system for non-contact micro-motion measurement of compliant nanopositioning stages and micromanipulators is proposed using computer micro-vision. The micro-motion measurement method integrates optical microscopy and an optical flow-based technique, in which the motions of complaint mechanisms are precisely detected and measured. Simulations are carried out to validate the robustness of the proposed method, while the micro-vision system and a laser interferometer measurement system are also built up for a series of experiments. The experimental results demonstrate that the proposed measurement system possesses high stability, extensibility, and precision with 0.06 µm absolute accuracy and 0.05 µm standard deviation.