Stimuli-responsive phosphorescence materials with dynamic color-changing properties are highly promising for advanced information security. Herein, we demonstrate a novel strategy that effectively induces tunable dynamic phosphorescence color from carbon dots (CDs) on papers via surface ionization engineering for multimode encryption and information storage. Alkali-induced phenolic hydroxyl ionization on CDs can boost intersystem crossing rates, while surface-ionized groups with negative charges significantly passivate the surface defects and reduce non-radiative transitions, which can activate surface state-related blue phosphorescence emission. Combined with the carbon core state-related yellow-green phosphorescence, excitation/time-dependent phosphorescence color-changing from yellow-green to blue are realized from alkali (NaCO) treated CDs on paper. Furthermore, benefiting from the transition from NaHCO to NaCO under thermal treatment, dynamic color-changing phosphorescence can also be activated by thermally stimulating NaHCO-treated CDs on paper. Finally, multi-stimuli (alkali or thermal) and multi-modal dynamic phosphorescent colors from a single CDs system are realized for the first time. Based on these unique features, multimode encryption and smart 3D codes with anti-counterfeiting and monitoring functions for medicine during transport or storage are demonstrated by combining an inkjet printing technique using CD inks.