The optical modulation of fluorescence characteristics in molecular aggregates, which mainly involves diverse molecular stacking and the consequent intermolecular interactions, remains a significant challenge for potential applications in optical anticounterfeiting, data storage, and imaging. Here we successfully realize in situ fluorescence switching in molecular aggregates of thianaphthene‐dioxide derivatives by topological [2+2] photocycloaddition, which represents a promising way to regulate the molecular stacking and alter photophysical processes. Notably, 2‐(3,5‐bis‐trifluoromethylphenyl)benzo[b]thiophene‐dioxide (BTO‐TF) in both crystal and powder forms exhibits a unique switching from an initial nonfluorescent state to a highly fluorescent state (ΦPL=0.46) upon UV irradiation, because of the destruction of the [2+2] cycloaddition process by volume expansion of the photodimer. Furthermore, we demonstrate such a [2+2] photocycloaddition can occur when 2‐(4‐carboxypheny)benzo[b]thiophene‐dioxide (BTO‐OH) is doped within selective polymer matrixes, and can be utilized for the visualization of macrophase separation in polymer blends.