Oligo(phenylene ethynylene)s (OPEs) are widely used as conductive building blocks in molecular electronics. It is known that a phenylene unit in OPEs has low energy barrier (100 meV) for its rotation along the axis of the molecule. We have modeled an OPE-based molecular junction where an OPE oligomer is connected between conducting leads, and calculated the conductance of the junction using gDFTB code. We show that the conductance at the Fermi energy significantly changes as a function of rotation angle of the phenylene unit yielding the on/off ratio over 104. We have also performed the ab initio MD at room temperature and obtained the similar result. This result implies that a special attention needs to be paid to the relationship between conductance and fluctuation of molecular framework.