We report the process of intensified preparation of ultrasmall and monodisperse selenium-doped carbon dots (Se-CDs) by using an internal circulation rotating packed bed (IC- RPB) as the reactor, in which the micromixing and mass transfer for reactants are highly enhanced. Compared with the Se-CDs prepared in a typical autoclave (without stirring) and stirred tank reactors, the Se-CDs obtained in the IC-RPB reactor are significantly reduced in size (2 nm). The ultrasmall Se-CDs exhibit excellent monodispersity with bright green luminescence under irradiation of UV light. The quantum yield of newly developed ultrasmall Se-CDs is 11.35%, which achieves a new record on the basis of reports previously. The ultrasmall Se-CDs show low cytotoxicity and can easily get inside the cells, endowing with capacity for in vitro bioimaging. Furthermore, the Se-CDs could be used as favorable free radical scavengers due to the dose-dependent cytoprotective capability against oxidative damage induced by H2O2.