The invention provides a magnetic navigation motor structure based on a functionally graded material. A first current source is connected with the positive electrode of a first Helmholtz coil and thepositive electrode of the first Helmholtz coil, and a second current source is connected with the positive electrode of a second Helmholtz coil and the positive electrode of the second Helmholtz coil.The Helmholtz coils are electrified to generate a uniform magnetic field, and the functionally graded material is placed in the uniform magnetic field. Through the above settings, the structure achieves the effective reduction of the number of external coils of a human body, enlarges a detection space, just needs to two current sources, is simple, and has fewer control parameters.