It is observed in test operation that for permanent magnet electro-magnetic suspension (PEMS) type high speed maglev train, when a single levitation unit in an end joint structure fails to work, the performance of the entire joint structure deteriorates rapidly, whereas in electro-magnetic suspension (EMS) type maglev system, there is no such phenomenon under the same failure. To solve this problem and to enhance system performance under faulty condition, firstly a comparative modeling of EMS and PEMS maglev end joint structure system was made to analyze the underlying reasons. Then a dynamic compensation method and a disturbance rejection method based on disturbance estimation and feedback linearization were proposed respectively. The performances of the proposed measures are verified and compared in simulations.