The direct laser writing (DLW) of photoluminescent metal clusters is inspiring intensive research in functional glasses. However, the impact of the host structure on cluster formation and visualization of DLW-induced clusters at the atomic scale remains challenging. In this work, we developed a highly photosensitive fluorophosphate glass matrix through fluorine incorporation. The addition of fluorine established a conducive environment for Ag+ ions before DLW and enhanced the availability of reducing agents and diffusion pathways during DLW. These advantages facilitate the formation of Ag quantum clusters (Ag QCs) dots under low-energy single-pulsed DLW. Increasing laser energy resulted in a combination of Ag QCs and glasses defect, forming a dot + ring photoluminescent pattern. To directly visualize the Ag QCs, we employed atom probe tomography (APT), a technique capable of mapping the spatial distribution and quantifying the number of Ag QCs. APT results demonstrated that DLW effectively halves the distance between adjacent Ag+ ions, leading to a significant increase in the abundance of Ag QCs with various aggregations, as well as a 31-fold increase in cluster density. The design concept and characterization enrich our understanding of Ag QCs behavior in glasses. This new knowledge opens up possibilities for the rational design of clusters confined in glasses and inspires their directed synthesis and various applications.