Track mis-registration (TMR) is one of the major problems in high-density magnetic recording systems such as bit-patterned media recording (BPMR). In general, TMR results from the misalignment between the center of the read head and that of the main track, which can deteriorate the system performance. Although TMR can be handled by a servo system, this paper proposes a novel method to alleviate the TMR effect, based on the readback signal. Specifically, the readback signal is directly used to estimate a TMR level and is then further processed by the suitable target and equalizer designed for such a TMR level. Simulation results indicate that the proposed method can sufficiently estimate the TMR level and then helps improve the system performance if compared to the conventional receiver that does not employ a TMR mitigation method, especially when an areal density is high and/or a TMR level is large.