We consider uniqueness problems for meromorphic inner functions on the upper half-plane. In these problems, we consider spectral data depending partially or fully on the spectrum, derivative values at the spectrum, Clark measure, or the spectrum of the negative of a meromorphic inner function. Moreover, we consider applications of these uniqueness results to inverse spectral theory of canonical Hamiltonian systems and obtain generalizations of the Borg-Levinson two-spectra theorem for canonical Hamiltonian systems and unique determination of a Hamiltonian from its spectral measure under some conditions.
