Distinguishing structural isomers at the single-molecule level remains a challenge. We report the single-molecule recognition of two diketopyrrolopyrrole containing isomers (SDPP and SPPO) employing the mechanically controllable break junction technique. The single-molecule conductances of the two isomers are indistinguishable under normal conditions. However, reversible protonation and deprotonation of the SPPO in molecular junction result in more than 1 order of magnitude conductance change, which dramatically enhances the conductance difference between the two isomers. Theoretical study reveals that the dramatic conductance switching is due to reversible quantum interference effect. It is suggested that combination of stimuli-response and quantum interference can be an efficient strategy to enhance isomer recognition and conductance switching in single-molecule junctions.