The invention relates to a miniature eddy current sensor with a structure consisting of a silicon substrate and multilayer coils, and belongs to the field of miniature sensors. The miniature eddy current sensor is used for detecting micro-cracks on surfaces of metal components, is based on the three-inch silicon substrate with the thickness of 200 micrometers and comprises a single-layer excitation coil, multiple layers of detection coils, conducting layers and insulating layers, each two layers of detection coils are serially connected and communicated by a central lead in a reverse spiral surrounding manner, flow directions of induced currents of the detection coils are consistent assuredly, and detection signals are intensified; and each silica insulating layer is filled between the corresponding detection coil and the excitation coil. The size of the section of each detection coil can be 10 micrometers X 10 micrometers, 20 micrometers X 15 micrometers and 30 micrometers X 15 micrometers, each coil includes 10 turns, the corresponding size of the section of the excitation coil can be 140 micrometers X 20 micrometers, 290 micrometers X 20 micrometers and 430 micrometers X 20 micrometers, and the excitation coil includes a single turn. The inductance coils are squarely or circularly spiral in a planar manner, and are distributed in a matrix manner according to the shapes and the sizes of the inductance coils, so that detection area is increased, and detection efficiency is improved. By the aid of via UV-LIGA (ultraviolet-lithography) which is precision processing technology on the basis of a micro-electro-mechanical system MEMS, the miniature eddy current sensor has the advantages of slim structure, miniaturization and high sensitivity and efficiency, and is applicable to nondestructive detection of microdefects on surfaces of metal workpieces.