Controlling the macroscopic organization of self-assembled peptide nanostructures on a solid surface is a key challenge in enabling their technological applications. Here, we report a simple approach to achieve the horizontally organized self-assembly of dipeptides by introducing graphene sheets. We show at the first time the formation of a macroscopic-scale, high-density, and ordered interlaced array of peptide nanowires and graphene composite (PNWs-G) on a silicon surface under mild conditions. The action of graphene sheets in the formation of the organized bionanostructure was preliminarily investigated. Furthermore, due to the introduction of graphene, the electronic conductivity of the bionanostructures was greatly improved, which is very beneficial for their applications in bioelectrochemical and nanoelectronic devices. As an applied example, the significantly enhanced electrochemical sensing performance for dihydronicotinamide adenine dinucleotide (NADH) was also demonstrated at the PNWs-G modified electrode relative to the alone component and unordered composite modified electrodes. The simple and mild approach described, here opens a new avenue for the fabrication of macroscopic-scale organized self-assembled peptide bionanostructures on a solid surface, which should be capable of being extended to other biosystems based on graphite surface-template assembly, allowing a variety of functional bionanostructures to be fabricated and used in practical applications.