Manufacturing method and manufacturing system of Josephson junction device

The invention provides a Josephson junction device manufacturing method and system, and the method comprises the steps: forming a laminated structure which is formed by sequentially laminating a first film layer, a second film layer and a third film layer on a substrate, enabling the laminated structure to be provided with a mask layer, carrying out the etching of the third film layer through employing the mask layer as a mask, and removing the mask layer through the etching of target gas, according to the Josephson junction, the mask layer does not need to be removed by using a wet process, the problems of contamination of the surface interface of the film layer, oxidation of the side wall of the third film layer and the like caused by wet photoresist removal can be avoided, the electrical property of the Josephson junction is improved, an etching byproduct can be formed when the third film layer is etched and the mask layer is etched by using target gas, and the etching efficiency is improved. When the Jose