The present invention discloses a preparation method of a superconductive Josephson junction. belonging to the field of superconducting circuit elements. The method comprises the steps of: 1) performing preprocessing of a substrate, and obtaining a clean substrate; 2) performing electron beam exposure: coating electron beam glue on the substrate, and employing an electron beam exposure device to expose an area A and a area B on the substrate, wherein an area C is arranged at the intersection of the area A and the area B; 3) performing development: putting a container holding developing solventinto liquid, monitoring a temperature of the developing solvent, immersing the substrate obtained in the step 2) into the developing solvent and performing shaking development when the temperature ofthe developing solvent reaches a fitting temperature and is stably remained at the temperature, and then performing fixing, and allowing a figured formed by the electron beam glue to be stabilized; 4) performing inclined evaporation coating twice; 5) performing metal peeling. The preparation method of the superconductive Josephson junction employs an electron beam exposure mark technology and anelectron beam coating and metal peeling technologies, is relatively simple in process, avoids a complex suspension colloid preparation process and can perform batch preparation of superconductive Josephson junction samples in one day.