To improve the output torque in permanent magnet (PM) eddy current couplings, a new structure based on harmonics injection into the magnet optimization theory is proposed. Then, a novel analytical electromagnetic-thermal model is established that can accurately reflect the 3-D distributions of the magnetic field and the eddy current. With the proposed analytical model, the eddy current loss, temperature distribution, torque characteristics and influence of the temperature rise caused by load increases on the torque are predicted and analyzed precisely. The maximum output torque can be improved by 11.22% with injected harmonics into the magnet shape. On this basis, an optimal design of the conductor plate structure is presented, based on the electromagnetic-thermal analytical model. An additional 13.05% torque improvement can be obtained, which leads to better torque characteristics and overload capability. Verification is conducted by a 3-D finite element analysis and measurements. The analytical model solves the multiphysics coupling analysis problem of PM eddy current couplings, and provides a fast and accurate calculation method to perform electromagnetic-thermal coupling analysis. INDEX TERMS PM eddy current couplings, torque improvement, eddy current loss, electromagneticthermal model.