Water-soluble red afterglow imaging agents based on ecofriendly nanomaterials have potential application in time-gated afterglow bioimaging due to their larger penetration depth and nondurable excitation. Herein, red afterglow imaging agents consisted of Rhodamine B (RhB) and carbon nanodots (CNDs) have been designed and demonstrated. In these agents, CNDs act as energy donors, and RhB acts as an energy acceptor. Both of them are confined into a hydrophilic silica shell to form a CNDs-RhB@silica nanocomposite. The phosphorescence emission spectrum of the CNDs and the absorption spectrum of the RhB match well, and efficient energy transfer from the CNDs to the RhB via Förster resonant energy transfer process can be achieved, with a transfer efficiency can reach 99.2%. Thus, the as-prepared nanocomposite can emit a red afterglow in aqueous solution, and the afterglow spectrum of CNDs-RhB@silica nanocomposite can extend to the first near-infrared window (NIR-I). The luminescence lifetime and afterglow quantum yield (QY) of the CNDs-RhB@silica can reach 0.91 s and 3.56%, respectively, which are the best results in red afterglow region. Time-gated in vivo afterglow imaging has been demonstrated by using the CNDs-RhB@silica as afterglow agents.