We explore the holographic phase transition with logarithmic nonlinear electrodynamics in the backgrounds of the AdS soliton away from the probe limit. We disclose the properties of phases by the holographic entanglement entropy of disk for the scalar operators. We find that the holographic entanglement entropy is a useful tool to probe the critical chemical potential and the order of the phase transition in the system. In the superconductor phase, the holographic entanglement entropy for scalar operator <O+> has a non-monotonic behavior as the chemical potential increases, while the entanglement entropy for operator <O−> decreases monotonously. With the increase of the logarithmic nonlinear factor b, the holographic entanglement entropy becomes bigger for both scalar operators <O±>. Furthermore, the insulator/superconductor phase transition probed by the entanglement entropy in the holographic system is characterized only by the chemical potential and is independent of the logarithmic nonlinear electrodynamics.