In this paper, the subdomain analysis model of the eddy current brake (ECB) is established. By comparing with the finite element method, the accuracies of the subdomain model and the finite element model are verified. Furthermore, the resistance characteristics of radial, axial, and Halbach arrays under impact load are calculated and compared. The axial array has a large braking force coefficient but low critical velocity. The radial array has a low braking force coefficient but high critical velocity. The Halbach array has the advantages of the first two arrays. Not only the braking force coefficient is large, but also the critical speed is high. The parameter analysis of the Halbach array is further carried out. The inner tube thickness and air gap length are the sensitive factors of resistance characteristics. The demagnetization effect is significantly enhanced by the increase of the inner tube thickness. In order to ensure that the ECB does not overheat, the electromagnetic-thermal coupling model is established based on the heat transfer theory. The temperature rise of the inner tube is obvious while that of the permanent magnet is small. The temperature rise of the inner tube is more than 20 K each time, and that of the permanent magnet is less than 1 K each time.