In the present study, the atomistic approach, developed previously by hybridizing both internal energies and atomic-scale defect structures, is extended to predict the trend of glass forming ability (GFA) from the Zr–Cu binary alloy system with good GFA to the Zr–Ni binary system with relatively poor GFA. The predicted composition dependence of the GFA in the Zr–Ni alloy system is consistent with those obtained from experimental results, indicating the validity of the proposed atomistic approach in both of the alloy systems. The different GFAs in the Zr–Cu and Zr–Ni systems have been puzzled by the metallic glass community for quite a long time, and our study provides the physical reasons for the different glass forming behaviors of the two alloy systems in terms of both atomic configurations and relative stability of their intermetallic phases.