Supported lipid bilayers (SLBs) are artificial lipid bilayers at solid–liquid interfaces applied as cell membrane model systems. An advantage of the artificial system is that the lipid composition can be controlled arbitrarily. On the other hand, the SLB formation process and its efficiency are affected by the properties of the solid substrate surface. In this study, we investigated the effect of the electrostatic interaction between the negatively charged SiO2/Si substrate surface and the lipid bilayer membrane on the composition of binary SLBs comprising anionic and neutral lipids. The phase transition temperature and the area fraction of lipid domains of SLB were evaluated by fluorescence microscopy and the fluorescence recovery after photobleaching. The neutral lipid was preferably included in SLB, but the anionic lipid ratio increased with Ca2+ concentration during the SLB formation. The lipid composition in SLB can be controlled by modulating the substrate-induced electrostatic potential.