Well-ordered silver nano arrays, prepared using anodic aluminum oxide (AAO) template by laser molecular beam epitaxy (L-MBE) method, were adhered to the work electrode using conductive adhesive to be a Surface-enhanced Raman scattering (SERS) substrate. Variable SERS signals of paranitrobenzoic acid (PNA) on the electrode modified with silver nano arrays were recorded with electric potential ranging from 0.1 to −0.5 V. The SERS spectra of PNA using DFT-B3PW91 with lanl2dz based on two models were calculated. It indicate that the adsorption orientation of probe molecules on the silver nano arrays with potential change of the electrode.Graphical abstractSurface enhanced Raman scattering spectra of probe molecules paranitrobenzoic acid were recorded on the electrode of silver nano arrays. The SERS spectra of PNA using DFT-B3PW91 with lanl2dz based on two models were calculated, and compared with the experimental results. It shows the adsorption transformation of probe molecules on the silver nano arrays with potential change of the electrode.Highlights► Well-ordered silver nano arrays prepared using AAO template by laser molecular beam epitaxy method. ► SERS spectra of probe molecules were recorded on silver nano arrays at potential ranging from 0.1 to −0.5 V. ► PNA SERS spectra were calculated based on two models, which indicates the adsorption orientation of PNA on the silver nano arrays with potential change of the electrode.