For electronic transport at the nanoscale, coherent scattering at defects plays an important role. Therefore, the capability of visualizing the influence of defects on the conductivity of single atomic junctions may benefit the development of future nano-electronics. Here, we report imaging the coherent scattering from a defect with well-controlled geometry by quantum point contact microscopy recently developed by us. An similar to 10% modulation in transport conductance of a single atomic junction is observed, with a phase shift of nearly p compared to the tunneling conductance. With the well-defined scattering geometry, we performed a theoretical calculation of the conductance and found the result consistent with the experiment.