Carbon dots (CDs) with red-emitting room-temperature phosphorescence (RTP) are rarely reported because of the increasing nonradiative decay of the excited states and the decreasing energy gap between the excited states and ground states. Herein, we demonstrate a facile strategy for modulating the RTP properties of CDs in terms of donor-acceptor energy transfer (EnT) in the CDs-in-zeolite system. Upon tuning of the heteroatoms (Zn2+, Mn2+) doped in the aluminophosphate zeolite frameworks, CDs@zeolite composites with green and red phosphorescence have been prepared via in situ hydrothermal synthesis. In such composites, the zeolite matrix provides an efficient confinement role in stabilizing the triplet states of CDs. Significantly, the Mn-doped zeolite could act as an energy acceptor allowing EnT from excitons of CDs to the dopant in the host matrix, generating the intriguing red RTP behavior. This work provides an effective strategy for developing CD-based composite materials with special RTP emissions as well as new fields for applications.