The invention discloses design of a special superconductor low-temperature cooling structure applied to a superconductive magnetic suspension micro thrust measurement system. The superconductor low-temperature cooling structure comprises a refrigerator, a cooling base, a cooling copper column, a cooling copper ring, a superconductive stator array, an Al<2>O<3> ceramic cover plate, an indium sheet, graphite gaskets, an anti-radiation screen and the like. Specific to the requirements of high cooling efficiency and low eddy current loss of the cooling structure of the measurement system, a dual-path conduction cooling structure with low eddy current effect is designed; according to the cooling structure, the heat conduction gaskets capable of lowering contact heat resistance are arranged on the respective contact surfaces of corresponding parts, and by virtue of setting of the anti-radiation screen, radiation heat flow from the exterior can be isolated; and when the measurement system is in use, the Al<2>O<3> ceramic cover plate and the graphite gaskets with a weak eddy current effect are positioned in a region with severe magnetic field changes, while the cooling base, the cooling copper ring and the cooling copper column with an obvious eddy current effect are isolated from the region, so that the eddy current loss of the conduction cooling structure is suppressed by virtue of the conduction cooling structure layout.