Crystalline phase evolution through merely adjusting composition was achieved in silicate glass ceramics containing LunOn-1Fn+2 (n = 5–10) nanocrystals. Orthorhombic or cubic phase nanocrystals were precipitated in the aluminosilicate glass matrix after thermal treatment together with varying the Na2O/NaF ratio. Oxyfluoride nanocrystals with quasi-spherical shape show homogenous and dense distribution in glass matrix by transmission electron microscopy measurement. Intense upconversion and mid-infrared emissions were realized in these glass ceramics compared to the precursor glass, and the emission spectral shapes, relative emission intensity and fluorescence decay curves of Er3+ in cubic LuOF embedded samples exhibit remarkable differences due to the crystal phase dependent effect in glass ceramics. These results indicate that the crystallization and luminescence properties of oxyfluoride glass ceramics could be modified through the alteration of glass composition, which could be used for the development of novel glass ceramics and design of luminescent properties.