The invention relates to the processing technology of ionizing radiations, in particular to X-ray focusing apparatuses applying diffraction, refraction or reflection, and specifically to a preparationmethod of an adjustable waveguide system for X-ray nano-scale focusing. The waveguide system comprises an adjustable shell matrix, the adjustable shell matrix consists of a first shell matrix and a second shell matrix, the first shell matrix and the second shell matrix can be driven to carry out relative movements, the interiors of the first shell matrix and the second shell matrix are both fixedly provided with multi-layer thin film waveguide structures with a same structure, and the adjustable shell matrix is integrally arranged in a temperature-adjustable cavity. Compared with the prior art, the adjustable waveguide system can use two waveguide structures to perform regulatory focusing on X-ray, and the problem that the expected focusing effect cannot be achieved in a traditional focusing apparatus is solved, because after the traditional focusing apparatus is produced and formed, errors existing in a manufacturing process of the traditional focusing apparatus can cause parameter differences comparing with parameters determined by a simulation calculation process, so that a novel idea for further improving the focusing performance of X-ray waveguides is provided.