Negative thermal quenching effect (TQE) refers to a phenomenon that the luminescence intensity increases as the temperature increases, which is reported in a few rare-earth doped upconversion (UC) nanocrystals (NCs). However, it is still difficult to enhance the negative TQE for those NCs without changing the particle size. Herein, through comparing the temperature dependent UC emission intensity variations between the Yb/Er co-doped CaF2 and BaF2 NCs as well as the CaF2:Yb/Er and BaF2:Yb/Er based core/shell NCs with different shell layers, we verify that the negative TQE can be improved by employing the matrix with lower phonon energy owing to the reduced possibility of the multi-phonon assisted non-radiative relaxation. This novel method for the improvement the negative TQE may found potential applications in anti-counterfeiting and temperature sensing fields.