In this work, we perturbatively calculate the modular Hamiltonian to obtain the entanglement entropy in a free fermion theory on a torus with three typical deformations, e.g., $$ T\overline{T} $$ T T ¯ deformation, local bilinear operator deformation, and mass deformation. For $$ T\overline{T} $$ T T ¯ deformation, we find that the leading order correction of entanglement entropy is proportional to the expectation value of the undeformed modular Hamiltonian. As a check, in the high/low-temperature limit, the entanglement entropy coincides with that obtained by the replica trick in the literature. Following the same perturbative strategy, we obtain the entanglement entropy of the free fermion vacuum state up to second-order by inserting a local bilinear operator deformation in a moving mirror setting. In the uniformly accelerated mirror, the first-order and second-order correction of entanglement entropy vanishes in the late time limit. For mass deformation, we derive the entanglement entropy up to first-order deformation and comment on the second-order correction.