Being chosen as a differential operator of a special form, metric $eta$ operator becomes unitary equivalent to a one-dimensional Hermitian Hamiltonian with a natural supersymmetric structure. We show that fixing the superpartner of this Hamiltonian permits to determine both the metric operator and corresponding non-Hermitian Hamiltonian. Moreover, under an additional restriction on the non-Hermitian Hamiltonian, it becomes a superpartner of another Hermitian Hamiltonian.