Understanding the relationships between the molecular structure and electronic transport characteristics of single-molecule junctions is of fundamental and technological importance for future molecular electronics. Herein, we report a combined experimental and theoretical study on the single-molecule conductance of a series of oligo(phenylene ethynylene) (OPE) molecular wires, which consist of two phenyl–ethynyl–phenyl π units with different dihedral angles. The molecular conductance was studied by scanning tunneling microscopy (STM)-based break-junction techniques under different conditions, including variable temperature and bias potential, which suggested that a coherent tunneling mechanism takes place in the OPE molecular wires with a length of 2.5 nm. The conductance of OPE molecular junctions are strongly affected by the coupling strength between the two π systems, which can be tuned by controlling their intramolecular conformation. A cos2 θ dependence was revealed between the molecular conductance and dihedral angles between the two conjugated units. Theoretical investigations on the basis of density functional theory and nonequilibrium Green’s functions (NEGF) gave consistent results with the experimental observations and provided insights into the conformation-dominated molecular conductance.