In mechanical bionics field, it is necessary to measure the bionic prototypes generated milli-micro force. To satisfy the test requirement, a milli-micro Newton two-dimensional force measuring system was designed. Hardware of the system mainly includes self-developed parallel double spring cantilevers and its matched eddy current displacement sensors, milli-micro force measurement platforms which can realize the easy installation of samples, transducer output signal conditioning module and data sampling card, and data processing and displaying program based on LabVIEW. To test the system function, the system operation debugging was implemented. The friction force, the normal force, and the piercing resistance force provided by the bionic prototypes were measured. The results confirm that the system can obtain these force values with milli-micro magnitude accurately, and display these force values in real time and intuitively in the interface window, as well as realize the storage of these force values in the form of force trajectory diagram and data group effectively. Accuracy and range of this milli-micro Newton two-dimensional force measuring system is respectively up to 50 μN and 800 mN. Our designed system can accurately measure the milli-micro Newton two-dimensional force produced by bionic prototypes, and provide the technique and method of force measurement used in mechanical bionics.