Fluoroaluminosilicate glass-ceramics with M 1 − x R x F 2 + x (M 2+ : Sr 2+ , Ba 2+ , R 3+ : rare earth ions) crystals are novel host materials for luminescence applications. However, the preparation of such materials is still a trial-error based approach due to the lack of detailed glass structure understanding. In this work, the authors study the phase separation and potential nanocrystal formation in a series of Ba 2+ and La 3+ containing fluoroaluminosilicate glasses by molecular dynamics (MD) simulations. Fluoride phase separation is observed from all simulated glass samples. With gradual LaF 3 to BaF 2 substitution, the cations enrichment changes from Ba 2+ , to Ba 2+ and La 3+ , and finally La 3+ in the fluoride-rich regions. Besides, the competition between Al 3+ and La 3+ in fluoride phase and the consequently redistribution of Al 3+ and Na + into oxide phase are observed, which can change the local environment of luminescent centers, affecting luminescence. An experimental support to this phenomenon is given. Therefore, MD simulation with effective potentials can be a practical method to study the structural origins of nanocrystal from fluoride phase separation as well as to study the structure-property relationship in fluoroaluminosilicate glass. The simulation driven glass structure and crystal phase exploration can thus become an effective method in designing glass-ceramics for luminescence and other applications.