A deep understanding of how the host matrix influences the afterglow properties of molecule dopants is crucial for designing advanced afterglow materials. Despite its appeal, the impact of defects on the afterglow performance in molecule-doped SiO2 matrices has remained largely unexplored. Herein, we detail the synthesis of monodisperse SiO2 microparticles by hydrothermally doping molecules, such as 4-phenylpyridine, 4,4'-bipyridine, and 1,4-bis(pyrid-4-yl)benzene. Our results demonstrate that hydrothermal reactions induce not only the formation of emissive defects in the SiO2 matrix but also enable molecule doping through SiO2 pseudomorphic transformation. Optical analyses reveal a remarkable afterglow activation of doped molecules, driven by a synergistic interplay of hydrogen bonding and physical fixation. Specifically, 4-phenylpyridine doping leads to an impressive 227- and 271-fold enhancement in fluorescence and afterglow, respectively, and an extraordinary 3711-fold enhancement in the afterglow lifetime of the resulting SiO2 MPs. We also document hybrid states involving molecule dopants and SiO2 defects, explaining energy transfer from molecule dopants to defects in both singlet and triplet states. The robust achievement of molecule doping provides flexibility to tailor excitation-dependent afterglow attributes while preserving angle-dependent structural colors, facilitating the creation of diverse building blocks for multiscale optical platforms for afterglow modulation and information encoding.