We report a simple and yet effective method to introduce Mn2+ ions into semiconducting nanoclusters with atomically precise control. Our method utilizes one type of micrometer-sized crystals, composed of well-defined isolated supertetrahedral chalcogenide nanoclusters (similar to 2 nm, [Cd6In28S52(SH)(4)]) whose core metal site is unoccupied in as-synthesized pristine form. This unique model structure with vacant core site makes it possible to achieve ordered distribution of Mn2+ dopants, and at the same time effectively preclude the formation of Mn2+ clusters in the host matrix. A two-step synthesis strategy is applied to realize an atomically precise doping of Mn2+ ion into the core site of the nanoclusters, and to achieve uniform distribution of Mn2+ dopants in the crystal lattice. The PL, X-ray photoelectron (XPS), as well as the electron paramagnetic resonance (EPR) spectra reveal the successful incorporation of Mn2+ ion into the core site of the nanocluster. Different from the pristine host material with weak green emission (similar to 490 nm), the Mn2+-doped material shows a strong red emission (630 nm at room temperature and 654 nm at 30 K), which is significantly red-shifted relative to the orange emission (similar to 585 nm) observed in traditional Mn2+-doped II-VI semiconductors. Various experiments including extensive synthetic variations and PL dynamics have been performed to probe the mechanistic aspects of synthesis process and resultant unusual structural and PL properties. The quaternary semiconductor material reported here extends the emission window of Mn2+-doped 11 VI semiconductor from yellow-orange to red, opening up new opportunities in applications involving photonic devices and bioimaging.