Tandem balloon system provides a solution to the problem of long-duration station-keeping of near-space aerostat, and its contained super-pressure balloon needs to be adapted to specific load and boundary conditions. Based on the natural-shape equations, a numerical method of local shape optimization of the two poles of spherical super-pressure balloons is proposed. Through the smooth connection of the numerical solution generatrix segment and the arc generatrix segment, the complete generatrix of super-pressure balloon with a certain angle at two poles is obtained, which is symmetrical up and down. The stress distributions of the super-pressure balloons before and after the local shape optimization are analyzed by the finite element method, and the effectiveness of the local balloon shape optimization method is verified. On this basis, the key factors affecting the effectiveness of local balloon shape optimization are analyzed, including the arc length of the numerical solution generatrix segment, circumferential stress input condition, local shape, and the radius of the arc generatrix segment, providing an important reference for the selection of key parameters in the local shape optimization of spherical super-pressure balloon.