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A strategy is demonstrated for simultaneous phase/size manipulation, multicolor tuning, and remarkably enhanced upconversion luminescence (UCL), particularly in red emission bands in fixed formulae of general lanthanide-doped upconverting nanoparticles (UCNPs), namely NaLnF4:Yb/Er (Ln: Lu, Gd, Yb), simply through transition metal Mn2+-doping. The addition of different Mn2+ dopant contents in NaLnF4:Yb/Er system favors the crystal structure changing from hexagonal (β) phase to cubic (α) phase, and the crystal size of UCNPs can be effectively controlled. Moreover, the UCL can be tuned from green through yellow and to dominant red emissions under the excitation of 980 nm laser. Interestingly, a large enhancement in overall UCL spectra of Mn2+ doped UCNPs (∼59.1 times for NaLuF4 host, ∼39.3 times for NaYbF4 host compared to the UCNPs without Mn2+ doping) is observed, mainly due to remarkably enhanced luminescence in the red band. The obtained result greatly benefits in vitro and in vivo upconversion bioimaging with highly sensitive and deeper tissue penetration. To prove the application, a select sample of nanocrystal is used as an optical probe for in vitro cell and in vivo bioimaging to verify the merits of high contrast, deeper tissue penetration, and the absence of autofluorescence. Furthermore, the blood vessel of lung of a nude mouse with the injection of Mn2+-doped NaLuF4: Yb/Er UCNPs can be readily visualized using X-ray imaging. Therefore, the Mn2+ doping method provides a new strategy for phase/size control, multicolor tuning, and remarkable enhancement of UCL dominated by red emission, which will impact on the field of bioimaging based on UCNP nanoprobes.