  In this work, we study the holographic entanglement entropy in AdS$_3$
gravity with the certain mixed boundary condition, which turns out to
correspond to $T\bar{T}$-deformed 2D CFTs. By employing the Chern-Simons
formalism and Wilson line technique, the holographic entanglement entropy in
$T\bar{T}$-deformed BTZ black hole is obtained. We also get the same formula by
calculating the RT surface. The holographic entanglement entropy agrees with
the perturbation result derived from both $T\bar{T}$-deformed CFTs and cutoff
AdS$_3$. Moreover, our result shows that the deformed entanglement entropy for
large deformation parameter behaves like the entanglement entropy of CFT at
zero temperature. We also consider the entanglement entropy of two intervals
and study the effect of $T\bar{T}$ deformation on phase transition.
