The transport properties of junction systems that consist of an X-biphenyl-X (X ¼ O, S, Se, and Te) molecule sandwiched between two gold electrodes are studied using the nonequilibrium Green's function method based on the density functional theory. The end-group atom X has an influence on not only the interaction between the molecule and electrodes but also that between the two phenyl rings. Especially, the junction system with X ¼ O exhibits much different properties from the other Xs. The interaction between the molecule and electrodes is weaker and that between -type orbitals of the two phenyl rings, which mainly contributes to the transmission around the Fermi energy, is stronger. As a result, this system has a larger transmission around the Fermi energy and unusual behaviors, such as a negative differential conductance and a nonlinear potential drop, are observed. We also studied the dependence on dihedral angle between the two phenyl rings.