Transformation from Lu-based nanocrystals in hexagonal and cubic mixed phases to pure cubic phase was observed through adjusting the doping concentration of Mn2+. The mechanism for the phase transformation was discussed in detail. Studies on the time and frequency domain spectra indicated that the semi-pure red emissions in cubic Na5Lu9F32: 40% Mn2+, 20% Yb3+, 2% Ln3+ (Ln=Er3+, Ho3+) nanocrystals were caused by a two-step energy transfer between Mn2+ and Ln3+ ions. After incorporating of Mn2+ ions into the host lattices, the local symmetry around the luminescent ion was reduced, which induced the increase of radiative rates for transitions that were mainly contributed by electric dipole radiations. Considerable enhancements in upconversion and downconversion luminescence were accompanied. The result of the current study has great application potential in bioimaging and solar cells.