Advances in polymeric matrices with ultralong and color-tunable phosphorescence were recently made, but their luminescence mechanism was not yet thoroughly understood. The current experimental and theoretical studies show that the red-shift of phosphorescence spectrum is caused by increasing the C–N and C=O of carbon dots in the polymeric matrix. In addition, theoretical calculations explain the charge transfer and spin orbit coupling of carbon dots in a system containing different covalent bonds. The phosphorescence emission color and lifetime can be modulated, which is applied into triple anti-counterfeiting of photo-stimulated-dependent color, time-dependent color, and time-dependent phosphorescence lifetime. In the application, the phosphorescence color of carbon dots in the polymeric matrix can be varied from deep blue (431 nm) to red (620 nm) with a maximal lifetime of 2.02 s and a maximum phosphorescence quantum yield of 20.1%. This work provides a new direction for the development of carbon dots with efficient and color-tunable ultra-long phosphorescence. Display omitted •The phosphorescence color of carbon dots can be varied from deep blue (431 nm) to red (620 nm) with a maximal lifetime of 2.02 s and a maximum phosphorescence quantum yield of 20.1%.•Theoretical calculations explain the charge transfer and spin orbit coupling of carbon dots in a system containing different covalent bonds.•The phosphorescence emission color and lifetime can be modulated, which is applied into triple anti-counterfeiting.