TheWahlquist-Estabrook(WE)prolongationstructuresofmodifiedBoussinesq(MB)systemarestudiedfromthecoveringspointofview.Therealizationsandclassificationsofone-dimensionalcoveringsofthissystemareobtainedcompletely.MoreoverthesufficientandnecessaryconditionsforavectorfieldtobeanonlocalsymmetryofthissystemarealsodemonstratedintheWEprolongationstructures.