Yb3+/Tm3+-codoped NaYF4 nanocrystals with different phases (cubic α and hexagonal β) and morphologies (nanoparticles, nanorods, nanoplates) have been controllably fabricated by a convenient hydrothermal synthesis technique. Up-conversion emission peaks were observed at λ=450, 475, 645, and 700 nm, which were assigned to the 1D2–3F4, 1G4–3H6, 1G4–3F4, and 3F2–3H6 transitions of Tm3+ ions, respectively. By using a homemade detection system, the anisotropic polarized emission properties of individual NaYF4:Yb, Tm nanorods and nanoplates were investigated. The results indicated that the polarization emission ratio, ρ, of the 1G4–3F4 emission of individual NaYF4:Yb,Tm nanorods was 0.18, whereas the anisotropic polarization emission of individual NaYF4:Yb,Tm nanoplates could be neglected; this indicated that the size and morphology of the nanocrystal played an important role in the polarized emission properties. Investigation into the mechanism indicated that the dielectric mismatch was not the predominant mechanism for the polarized emission of individual NaYF4:Yb,Tm nanorods. The as-prepared NaYF4:Yb,Tm nanocrystals, with controllable morphology and anisotropic polarized emission properties, are expected to be widely applied as polarized light resources, bio-labels, photodetectors, and so forth.