We study the behaviors of entanglement entropy and vacuum expectation value of Wilson loop in the Stuckelberg holographic insulator/superconductor model. This model has rich phase structures depending on model parameters. Both the entanglement entropy for a strip geometry and the heavy quark potential from the Wilson loop show that there exists a "confinement/deconfinement phase transition. In addition, we find that the non-monotonic behavior of the entanglement entropy with respect to chemical potential is universal in this model. The pseudo potential from the spatial Wilson loop also has a similar non-monotonic behavior. It turns out that the entanglement entropy and Wilson loop are good probes to study the properties of the holographic superconductor phase transition.