• Eigenmode analysis is applied to the dynamical many-body near-field radiative heat transfer under an external magnetic field. • We identify near-field and far-field thermalization modes and the roles of magneto-resistance effect and directional heat flow. • The near-field mode can be largely slowed down by the magnetic field and is highly tunable via variation of the direction of the magnetic field. • The far-field mode is greatly enhanced by the magnetic field due to extra contribution of circular resonances. • The far-field mode is independent on the particle-particle near-field interaction, the spatial arrangement of the cluster and the direction of the magnetic field. In this work, we apply eigenmode analysis to the dynamical many-body radiative heat transfer (RHT) of an ensemble of magneto-optical (MO) nanoparticles under an external magnetic field. With the eigenmode analysis, we identify near-field and far-field modes of thermalization, each mode can dominate the dynamical many-body RHT depending on the temperature distribution of the nanostructures. The near-field thermalization modes, dominated by near-field RHT, tend to distribute the thermal energy uniformly through the ensemble at small time scales. The eigenmode analysis shows that the thermal magneto-resistance effect can slow down the near-field mode by an order of magnitude, which is highly sensitive to the direction of the magnetic field. The far-field mode is activated upon reaching uniform temperature distribution and occurs at much larger time scales, in which the nanoparticles thermalize with the background via far-field RHT, independent of the near-field interaction, the spatial arrangement of the ensemble and the direction of the magnetic field. The far-field mode, in contrast, can be greatly accelerated by the magnetic field due to the extra contribution of circular resonances. The eigenmode analysis also identifies circular thermalization modes in certain configurations, indicating the emergence of persistent directional heat flow and the thermal photonic Hall effect. Aided with eigenmode analysis, our work gives deep physical insights into the thermalization process of MO many-body nanostructures, revealing the important role of the magnetic field in the temporal and spatial control of many-body near-field RHT.