Extended Derjaguin-Landau-Verwey-Overbeek (DLVO) theory has been the most commonly used theory to analyze the adhesion of bacteria on a solid surface. The adhesion of Shewanella oneidensis MR-1 on an electrode surface would directly affect the electricity production performance of microbial fuel cells (MFCs). In this paper, an analytical method for the adhesion between electricigens and electrode surface was established and its feasibility was verified based on the extended DLVO theory. The surface free energy of gold microarray electrodes based on glass and polymethyl methacrylate (PMMA) substrates was elucidated using contact angles, and the total interaction free energy curve of electrodes and S. oneidensis MR-1 was analyzed. Because of the potential barrier of repulsive force of gold microarray electrodes based on glass substrate was easy to cross, the architecture of S. oneidensis MR-1 aggregation on the surface was dense and stable. By contrast, on PMMA substrate, S. oneidensis MR-1 could form a loose and unstable aggregation due to the high potential barrier of repulsive force. The theoretical analysis was consistent with the experimental results by observing the scanning electron microscope images of S. oneidensis MR-1 aggregation. The extended DLVO theory could well predict the adhesion of S. oneidensis MR-1 aggregation on the surface of gold microarray electrodes based on different substrates, providing guidance for electrode design and optimization of MFCs.