Employing long-lived luminescent materials to design a chemical sensing platform can eliminate real-time excitation and background fluorescence. However, the realization of long-lived emissions in aqueous media was limited to transition-metal complexes, doped quantum dots, organic crystals, and inorganic persistent phosphors, which suffer from the drawbacks of large size, expensive elements, and poor dispersibility. In this work, phosphorescent carbon dots (CDs) were covalently immobilized in a silica matrix (CDs@SiO2) to achieve afterglow emission in an aqueous dispersion. CDs@SiO2 with long lifetime (∼1.6 s) was utilized as an energy donor to fabricate nonradiative energy transfer systems with various organic dyes through the surface micelle self-assembly method. Benefiting from the high energy transfer efficiency between CDs@SiO2 and organic dyes, multicolor afterglow emissions were successfully obtained in aqueous media. As a proof of concept, a ratiometric phosphorescent probe using CDs@SiO2 as a donor and Hg2+-responsive rhodamine derivative as an acceptor was designed. Hg2+ triggered the energy transfer process between the donor-acceptor pair, leading to the sensitive detection of Hg2+ ions. The work presented here provides opportunities to develop chemical sensors with low background interferences and easily recognizable signals.