Variations in molecular electronic structures related to conformational change are exceedingly attractive because of their key role in the understanding and development of functional processes in molecular electronics and biology. We observed, for the first time, the novel phase switching of a photoactive isomeric molecule, N-(2-mercaptoethyl)-4-phenylazobenzamide (Azo molecule) at a single-molecule level, which exhibits a distinctive change in the conductive characteristic under scanning tunneling microscope (STM) measurement. In comparison with the results obtained by the measurement of photoactive isomerization of the isolated Azo molecule, which was performed also for the first time, the observed characteristics are attributed to the results of the trans and cis phase transformation of the Azo molecule, under the condition of an external electric field and current flow. A specific point is that the potential landscape of the system is controllable by the electric field and provides a conformational stability with asymmetric bias dependence resulting in rectification.