A suspension of ferromagnetic rod-like particles can be expected to exhibit strong magneto-rheological characteristics, which is a significantly important factor for application of magnetic particle suspensions to mechanical dampers and actuators. Hence, in the present study, we address a suspension composed of ferromagnetic rod-like particles in thermodynamic equilibrium. We here investigate the dependence of the phase change in aggregate structures on the various factors such as magnetic field strength, magnetic particle–particle interaction strength and volumetric fraction of magnetic particles. Monte Carlo simulations have been carried out to obtain results of snapshots, radial distribution function and order parameter of the system. In a weak applied magnetic field, the magnetic rod-like particles tend to aggregate to form raft-like clusters if the magnetic particle–particle interaction is much larger than thermal energy. If the magnetic field is increased, these raft-like clusters drastically dissociate into single-moving particles, that is, the phase change in aggregate structures arises. Moreover, the phase change in the aggregate structures is induced by the magnetic particle–particle interaction strength, from no cluster formation to long and thick chain-like clusters, in a strong applied magnetic field circumstance. As the length of the magnetic rod-like particles is increased, the orientational configuration comes to have a more significant effect on the cluster formation.