Novel glass-ceramics (GCs) containing polymorphic CaTa2O6: Er3+/Yb3+ nanocrystals are prepared by aerodynamic levitation method following with a heat-treatment of the precursor glasses (PG). Phase transition from cubic to orthorhombic crystal forms depending on the heat-treatment temperature is observed. The appearance of corresponding GCs changes gradually from transparent to translucent, and to opaque at last. The evolution of phase composition and microstructure is investigated by X-ray diffraction (XRD), Rietveld refinement and transmission electron microscopy (TEM). Both XRD refinement results and spectroscopic properties confirm the incorporation of the rare-earth (RE) ions into crystalline phases, including the decrease in unit cell parameters, significant enhancement of upconversion (UC) luminescence, obvious Stark splitting of UC and near-infrared (NIR) emission bands as well as the extension of lifetimes. Furthermore, the temperature-dependent UC and NIR luminescence of the GCs containing polymorphic CaTa2O6: Er3+/ Yb3+ nanocrystals are investigated. Based on fluorescence intensity ratio (FIR) technique, the thermally coupled levels (TCLs) (2H11/2/4S3/2), non-thermally coupled levels (NTCLs) (4S3/2/4F9/2) and Stark sublevels (4I13/2) of Er3+ ions are used for three-mode thermometry. The maximum absolute sensitivities of FIR(H/S) and FIR(S/F) are 3.8×10-3 and 3.7×10-2 K-1, respectively, which are much higher than previous reports. Beyond that, FIR(1500/1532) based on Stark sublevels of orthorhombic phase GC offers a complementary way for temperature sensing. These results suggest the potential application of the GCs in self-referenced optical thermometry.