The vibration of the micro-milling tool presents a significant chaotic vibration phenomenon, which has a great influence on the tool life and part machining precision, and is one of the basic problems restricting the improvement of machining efficiency and machining accuracy in micro-milling. To overcome the difficulty of the traditional vibration measurement method with the online measurement of micro-milling tool multi-dimensional vibration, a three-dimensional (3D) measurement method of the micro-milling tool is proposed based on multi-fiber array coding, which converts the tool space motion into a decoding process of the optical coding array employing the tool modulating the multi-fiber array encoding. A 6 × 6 optical fiber array was designed, and a 3D motion platform for micro-milling tools was built to verify the characteristics of the optical fiber measurement system. The measurement results show that the measuring accuracy of the system reached 1 µm, and the maximum linear error in x-, y-, and z-direction are 1.5%, 2.58%, and 2.43%, respectively; the tool space motion position measurement results show that the maximum measurement error of the measuring system was 3.4%. The designed system has unique coding characteristics for the tool position in the space of 100 µm3. It provides a new idea and realization means for the online vibration measurement of micro-milling tools.