We study the orbital magnetic quadrupole moment (MQM) in three dimensional higher-order topological phases. Much like electric quadrupole moment, which is associated with a charge response on the boundaries of a finite sample, the diagonal components of the MQM manifest as surface-localized magnetization and hinge currents. The hinge current is generally not equal to the difference of surface magnetizations that intersect at the hinge, and we show this mismatch is precisely quantified by the bulk MQM. We derive a quantum mechanical formula for the layer-resolved magnetization in slab geometries and use it to define the MQM of systems with gapped boundaries. Our formalism is then applied to several higher-order topological phases, and we show that the MQM can distinguish phases in some intrinsic and boundary-obstructed higher-order topological insulators. We then show that derivatives of the MQM with respect to the chemical potential can act as quantized topological invariants, similar to obtaining the 2D Chern number as a derivative of the magnetization with respect to the chemical potential. These invariants provide a new way to characterize 3D time-reversal breaking insulators that have vanishing magnetization.