The suspension system of the EMS (Electro-Magnetic Suspension) medium-and-low-speed maglev train is affected by the eddy current effect when the train is in motion. This is a crucial problem related to the improvement of train operation speed. In this article, this phenomenon is analyzed and the method of suppressing the eddy current effect is put forward. Firstly, theoretical analysis and experimental verification are carried out. It is worth mentioning that the experimental data, which thoroughly show how the suspension current changes with the maglev train speed under the influence of the eddy current effect, are collected and published for the first time, which strongly confirms the accuracy of the theoretical analysis. Secondly, an improved scheme to suppress the influence of the eddy current effect is proposed from the perspective of the rail structure for the first time and simulation results verify the effectiveness of the improved scheme. This research makes important progress on the improvement of the rail used in the maglev train.