A lateral thickness distribution control model for magnetron sputter-deposited coatings was established using shadow masks. The sputtering yield distributions were investigated in detail, particularly the variation trend from straight to curved tracks, based on the erosion profiles of rectangular targets. On this basis, a mathematical model for a planetary rotation system was established to simulate the thickness distribution of coatings on different substrates, including flat, spherical, and aspherical shapes, accurately. A shadow mask with multi-Gaussian outlines was proposed, and the coating thickness was effectively controlled according to specific distribution requirements by optimizing the profile parameters of the masks using a genetic algorithm. Flat and ellipsoidal substrates were used to prepare Mo and Si monolayer coatings to verify the effectiveness of this model. Although the diameters of the substrates were close to the lengths of the rectangular targets, the results showed that uniform coatings were obtained on the flat substrate, whereas the ellipsoidal substrate exhibited high-precision gradient coatings, with maximum deviations below 0.5%, which proved the validity of this approach.