The development of single‐system materials that exhibit both multi‐color room‐temperature phosphorescence (RTP) and thermally activated delayed fluorescence (TADF) with tunable afterglow colors and channels is challenging. In this study, we developed four metal‐free carbon dots (CDs) through structural tailoring and achieved panchromatic high‐brightness RTP via strong chemical encapsulation in urea. The maximum lifetime and quantum yield reached 2141 ms and 56.55%, respectively. Moreover, CDs‐IV@urea, prepared via core‐shell interaction engineering, exhibited a dual afterglow of red RTP at 622 nm and green TADF. The degree of conjugation and functional groups of precursors affected the binding interactions of the nitrogen cladding on CDs, which in turn stabilized triplet energy levels and affected the energy gap between S1 and T1 (ΔEST) to induce multi‐color RTP. The enhanced wrapping interaction lowered the ΔEST, promoting reverse intersystem crossing, which leads to phosphorescence and TADF. This strong core‐shell interaction fully stabilized the triplet state, thus stabilizing the material in water, even in extreme environments such as strong acids and oxidants. These afterglow materials were tested in multi‐color, time, and temperature multi‐encryption as well as in multi‐color in vivo bioimaging. Hence, these materials have promising practical applications in information security as well as biomedical diagnosis and treatment.This article is protected by copyright. All rights reserved