In order to construct flat-top magneto-optical isolators (MOIs), we have performed a theoretical study on the case of transmission-type one-dimensional magnetophotonic crystals (MPCs). We have introduced high performance MPC structures with flat-top responses and with the capability of adjusting to perfect MOIs. The adjustment is carried out by tuning the applied magnetic field. All introduced MOIs are sufficiently thin with acceptable transmission bandwidth. In the best case, we have achieved a 19.42 μm-thick perfect MOI with the flat-top width of 7.2 nm. For practical purposes, we have also considered the influence of the error in thickness of individual layers on the operational parameters of the MOIs and investigated the possibility of compensating the deviations by the magnetic adjustment.