Lipid bilayer membranes are known to exist as heterogeneous and dynamic structures where the molecules are always moving and fluctuating under physiological conditions. Magnetic field effects (MFEs) studied herein are phenomena in which the exciplex emission from an electron donor-acceptor dyad increases or decreases by applying an external magnetic field. The characteristic dependence of MFEs on the viscosity and polarity of the surrounding medium has been applied to investigate the local environments around the probe molecule. In this study, a novel MFE-based fluorescence microscopy technique was developed to explore the structural dynamics of lipid bilayer membranes. The vesicle formation during the membrane deformation was selectively visualized through the MFEs, thus allowing the extraction of information on the cellular dynamics at high temporal and spatial resolutions. This highly versatile and powerful technique is applicable to a wide range of areas, such as biology and material science.