Internal OH- defects always cause significant depletion of excitation energy for low upconversion efficiency; however, preventing the incorporation of OH- into the crystal lattice is very difficult during the synthesis of upconversion crystals. In this work, red upconversion emission is dramatically enhanced in Er3+-sensitized hexagonal NaLuF4 (β-NaLuF4) microcrystals through a collaborative effect of ion exchange and Tm3+ doping. The ion exchange can not only maintain the morphology very well but also strongly reduce the internal OH- defects, which can enhance the upconversion luminescence due to improved excitation energy harvesting and red to green (R/G) ratio due to intense cross-relaxation. Doping of Tm3+ as an energy trapping center not only regulates the red emission output but also reduces the excitation energy loss. β-NaLuF4:Er,Tm microcrystals after ion exchange exhibit stronger red upconversion emission compared with β-NaYF4:Er,Tm and β-NaGdF4:Er,Tm counterparts. Moreover, fluorescent labeling of the fingerprint pattern printed from β-NaLuF4:Er,Tm microcrystals with stable and intense red fluorescence has been demonstrated under 980 nm excitation.