The invention provides a key layer priority well bore structure design method, which comprises the following steps of S1, preparing data: determining a well bore structure design coefficient, and drawing a curve graph; S2, determining the tripping-in depth D2: 1 of the intermediate casing at the key position; taking the depth of the key position as a primary selection depth D20; 2) verifying whether the risk of differential pressure jamming exists in the technical casing running primary selection depth D20 or not, and obtaining a check depth D21 without the risk of differential pressure jamming; 3) checking whether the casing running check depth D21 has the risk of pressure leakage or not according to the overflow well killing condition, and obtaining the running depth D2 without the riskof pressure leakage; S3, the tripping-in depth D1 of the surface casing pipe is determined; and S4, the tripping-in depth D3 of the intermediate casing pipe located below the key layer is determined.The method has the beneficial effects that the method is suitable for well bore structure design of the oil-gas well with the sealing requirement for the specific stratum, the working efficiency is improved, the working time is shortened, the design accuracy is improved, and the method has good economic and technical value.