The use of organic nanomaterials in biomedical and optical devices has been widely studied. The key to improving the performance and stability of these devices is to control the fabrication process, which determines the phase stability and photophysical properties. In this study, fluorescence changes were observed during the reprecipitation process of mechanofluorochromic molecules of dibenzoyl(methanato)boron difluoride. The cyan-emission phase (C-phase) was first identified. The time evolution of the resolved fluorescence spectra revealed that the green-emission phase (G-phase) was formed from the amorphous phase with yellow emission via the C-phase, in addition to the direct formation of the G-phase. Combined with the results of the investigation into the thermal properties, the fluorescence changes clearly indicate a two-step nucleation process and Ostwald's rule of stages for polymorph transition, which enables us to not only provide guidance for controlling the fabrication process but also propose the ripening process for organic nanoparticle formation.