Abstract Novel upconversion nanocomposites with nanoporous structure were presented in this paper. Silica-coated cubic NaYF4:Yb3+, Tm3+ nanoparticles were first prepared. After annealing, monodisperse cubic/hexagonal mixed phases NaYF4:Yb3+, Tm3+@SiO2 nanoparticles were obtained, and the NaYF4:Yb3+, Tm3+ cores became nanoporous. To the best of our knowledge, the nanoporous structure in NaYF4:Yb3+, Tm3+@SiO2 nanocomposites was observed for the first time. They demonstrate increased upconversion emission compared with unannealed dense NaYF4:Yb3+, Tm3+ nanoparticles due to the appearance of the hexagonal NaYF4:Yb3+, Tm3+. The silica shell not only makes the nanocomposites possess bio-affinity but also protects the NaYF4:Yb3+, Tm3+ cores from aggregating and growing up. Thus the upconversion, nanoporous and bio-affinity properties were combined into one single nanoparticle. The nanocomposites have been characterized by X-ray diffraction (XRD), field-emission scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM), small angle X-ray diffraction (SAXRD) and emission spectroscopy. These multifunctional nanocomposites are expected to find applications in biological fields, such as biolabels, drug storage and delivery.