Stepped horizontal hole section is applied to stack-up 2 or more continual thin reservoirs with certain different height, which has the advantages of saving drilling investment and improving the production efficiency of the single well compared with ordinary directional well and horizontal well. The design of 3D stepped horizontal well trajectory was made by the analysis on the existing design model of stepped horizontal well and by the use of the constant tool face model. The upper and lower targets’ drift angle and azimuth angle are taken as the known quantity, the build-up rate and installation angle of deflecting tools as control factors. In addition, the drift angle and azimuth angle of flex point are the parameters to be computed. It is shown by the calculation sample that the designed 3D hole trajectory can be used for the design of stepped horizontal hole section.