Carbon dots (CDs) show great promise in cutting-edge applications. However, achieving efficient room-temperature phosphorescence (RTP) in these materials is extremely difficult, particularly achieving broadly tunable, multicolor RTP. Herein, CDs were synthesized through a one-step hydrothermal method, and their RTP was enhanced by embedding them within a boric acid (BA) matrix. A two-step sequential strategy was employed: the aggregation degree of CDs was first modulated, followed by the introduction of an energy-transfer mechanism. This strategy successfully expanded the afterglow emission from blue to pink (450–606 nm), achieving a redshift of up to 157 nm and a maximum afterglow lifetime of 2.01 seconds. Precise control over the aggregation degree of the CDs, along with aggregation-induced effects such as molecular orbital coupling and energy-level splitting, enabled fine-tuning of the afterglow color within a limited range. Subsequently, the energy-transfer strategy further expanded the afterglow color gamut, highlighting the flexibility and considerable design space of this approach. Owing to their tunable afterglow color, the CD@BA composites were applied to anti-counterfeiting labels, effectively demonstrating the significant advantages of such multicolor phosphorescent CD systems in the field of advanced information encryption.