The invention provides a superconducting circuit with a superconductive layer covered step area and a preparation method thereof. The method comprises following steps: 1) providing a substrate and forming a three-layer film structure on the substrate, wherein the three-layer film structure is formed by a first superconducting material layer, a first insulating material layer, and a second superconducting material layer which are successively arranged; 2) etching the second superconducting material layer, the first insulating material layer and the first superconducting material layer to form a bottom electrode and a Josephson junction; 3) forming a second insulating material layer on the structure surface obtained in step 2); 4) depositing bypass resistance material layer, and etching the bypass resistance material layer to form a bypass resistance; 5) depositing a third superconducting material layer, and etching the third superconducting material layer to form a wiring layer and a superconducting coating layer. By use of the method, the bypass resistance on the bottom electrode surface and the bypass resistance on the second insulating material layer surface are guaranteed to be conducted, and therefore, the open circuit fault is avoided, the stability of bypass resistance connectivity is guaranteed, and the work performance of superconducting circuit structure is increased.