The quantum interference effect in the charge transport through single-phenyl molecules received intensive interests from theory but remained as an experimental challenge. In this paper, we investigated the charge transport through single-molecule benzene dithiol (BDT) junction with different connectivities using mechanically controllable break junction (MCBJ) technique. By further improving the mechanical stability and the electronic measuring component of the MCBJ set-up, we obtained the conductance histograms of BDT molecules (BDTs) from the statistical analysis of conductance-distance traces without data selection. By tuning the connectivity, the conductance of BDTs is determined to be 10−1.2G0, 10−2.2G0 and 10−1.0G0 for para, meta, and ortho connectivity, following the trend that ortho-BDT>para-BDT>meta-BDT. Furthermore, the displacements of the junctions followed the trend that para>meta>ortho, suggesting the charge transport through the molecules via the gold-thiol bond. The different trends between conductance and displacement for different connectivities suggests the presence of destructive quantum interference effect on meta-BDT, which provides the experimental evidence for the quantum interference effect through single-phenyl molecular junctions.