The structure-property relationship of DAE-derivative (C5F-4Py) molecular isomers which involve ring-closed status and ring-open status is investigated by employing non-equilibrium Green’s function formalism combined with density functional theory. Molecular junctions are formed by the isomers connecting to Au (111) electrodes through the flanked pyridine groups. The difference of electronic structures caused by different geometry structures for the two isomers, especially the alternative single bond and double bond in ring-closed molecule, contributes the remarkable different low-bias conductance values. The LUMO orbitals of isomers are mainly channels to transport electron. In addition, the more electrons transferred to ring-closed molecular junction in equilibrium condition drop down the LUMO orbitals closer to the Fermi energy which may be to contribute larger conductance value at Fermi level. Our findings are help to understand the mechanism of the low-bias conducting mechanism of and are conductive to design of high performance molecular switching based on DAE or DAE-derivatives molecules.