In order to solve the problem that the super-pressure balloon in the near space tandem balloon system being subjected to special boundary and load conditions, a method for optimizing the local shape of the two poles of spherical super-pressure balloons under bidirectional tension based on the natural shape equations was 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 was obtained, which was symmetrical up and down. The stress distributions of the super-pressure balloons before and after the local shape optimization were analyzed by the finite element method, and the effectiveness of the local balloon shape optimization method was verified. On this basis, the key factors affecting the effectiveness of local balloon shape optimization were 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.