The identification of conformational isomers of the flexible molecule is challenging, owing to the rapid interconversion of isomers. By attaching two electrodes on a flexible molecule, cyclohexane, we accomplish the distinguishment of the two chair isomers of cyclohexane at room temperature using a single-molecule approach. The confinement effect of the attached electrodes not only plays an important role in identifying the chair isomers but also stabilizes the twist-boat intermediate that is showing a negligible distribution in the solution of cyclohexane.