Aiming at the problem that the layout design of air-terminations in multiple lightning rod systems relies too much on engineering experience, based on the principle of least cost, an optimization model for the layout of air-terminations in multiple lightning rod systems is established by taking height and installation position of the air-terminations as the optimization variables. An optimization method for the layout of multiple air-terminations based on the genetic algorithm is proposed. The effectiveness of the proposed optimization method is verified by typical design cases. The results show that the deviation of the height and position of the air-terminations obtained by this method is not more than 0.29 m. All the preset objects to be protected can be completely covered within the protection range of the multiple lightning rod systems, and the minimum distance between the protected objects and the boundary of the protection range is not more than 0.71 m, which can fully meet the needs of engineering applications.