One-dimensional quantum systems can be experimentally studied in recent nanotechnology like the carbon nanotube and the nanowire. We have considered the mathematical model of a one-dimensional Schrodinger particle with a junction and have analyzed the phase factor in the boundary condition of the junction. We have shown that the phase factor in the tunneling case appears in the situation of the non-adiabatic transition with the three energy levels in the exact Wentzel-Kramers-Brillouin analysis.