<p>Realizing multi-mode programmable dynamic tunable persistent luminescence within a single solid is promising for multi-dimensional information storage and encryption applications. However, coupling luminescent centers with differentiated defect states remains a challenge. Here we report transparent glass ceramics that exhibit photo/thermally dynamic tunable afterglow. A lithium-ion doping-assisted phase separation principle is developed to control the precipitation of defective non-stoichiometric nanocrystals (Zn_1.7SiO₄: Li) in glass matrix, constructing a biphasic microenvironment with differentiated defect states. The persistent luminescence color can be manipulated by simultaneously engineering the distributions of Mn²⁺ activators in the amorphous glass matrix and nanocrystals, and the mechanism is discussed. The developed transparent composites exhibit excellent hardness of up to 10 gigapascal and high thermal stability, which is applicable for harsh conditions. This work pioneers a strategy for modulating dynamic afterglow in a single solid and inspires more potential applications in muti-dimensional information storage and encryption.</p>