The structural optimization design of axial permanent magnet coupling (APMC) was investigated. Firstly, based on the linear layer model, the mathematical optimization model of APMC was established. The key structural parameters (air gap and thickness of copper disc) of the established model were selected as the design variables. And the lowest cost, the maximum output torque and the minimum eddy current loss were chosen as the optimization goals. Secondly, the chaotic search and self-tuning weights were introduced into the cuckoo search algorithm, and an improved cuckoo search algorithm was proposed. In addition, multi-objective problem was converted into single one by using fuzzy theory, which was solved by using improved cuckoo search algorithm. Finally, the curve of eddy loss along with rotation speed and the curve of output torque along with slip were drawn by using ANSYS simulation, respectively, and the performances of improved APMC were verified. An experimental platform was built to test the prototype, of which the output torque and efficiency under different working conditions were tested. The results showed that the proposed method was superior to the other methods, making the cost and eddy current loss decrease by 9% and 10%, respectively, and the output torque increase by 15%. The expected results were derived, which indicated that the proposed optimization method had high precision and strong engineering practicability. The method provides a feasible preliminary design for axial permanent magnet coupling, and can be applied to the field of other electromagnetic devices.