In nanoscience, molecular switches have played a significant role to deliver different control abilities to practical functions, whereas high-contrast luminescence switchable manipulation at nanoscale is still limited. Since the tuning for emission behavior with high contrast ratio strongly connects to numerous visualized sensing and optoelectronic applications, we here report that autonomous pH control can be enrolled to address a high-contrast molecular emission change at the nanoaggregated level, for gaining a flicker luminescence performance in aqueous media. Employing a BODIPY contained dynamic covalent dye, we find its luminescent signal and nanoaggregate size can be spontaneously adjusted in water. On this basis, high-contrast luminescence switching of the material can be achieved upon the alternate introduction of base and acid into the aggregation state. Such a behavior can be attributed to a pH triggered photo-induced electron transfer regulation process. The dye aggregates can be well endocytosed for bioimaging and its luminescent variation can be autonomously displayed as a flicker effect. These results provide new visions for the design and development of smart materials with a dynamic luminescence behavior.