Matrix immobilization has been proven to be a favored method for enhancing the phosphorescence of carbon dots (CDs), however, it remains a significant challenge to realize time‐dependent phosphorescence colors (TDPC) by embedding CDs with single emission center. In this study, we present a novel matrix‐controlling strategy to regulate the microenvironment of CDs by doping limited Mn2+ in zeolite. The surrounding environment influences the surface state of the CDs, leading to the formation of different excitons. At low temperatures, Mn‐coordinated CDs (C‐CDs) show fast‐decaying green phosphorescence, while non‐coordinated CDs (NC‐CDs) exhibit inherent slow‐decaying blue phosphorescence. Notably, the energy transfer occurs between NC‐CDs and Mn2+ to produce an ultrafast‐decaying red phosphorescence, with the intensity of the red component increasing as the temperature rises. The interplay of these luminescent centers with distinct decay rates activates fascinating multi‐mode TDPC behavior as the temperature changes, resulting in dynamic afterglow evolutions from red to green at 298 K, orange to green at 273 K, and green to cyan to blue at 77 K. Leveraging the diverse luminescence of CDs@MnAPO‐5, a multi‐dimensional dynamic afterglow color pattern was developed for advanced anti‐counterfeiting applications.