Despite its significance in both fundamental science and industrial applications, the glass-forming transition in the Al2O3-Y2O3 (AY) refractory system is not yet fully understood due to the elusive structure evolution upon cooling. Here, atomic-scale structural changes in AY-bearing melts with different compositions and temperatures are tracked by employing in situ high-energy synchrotron X-ray diffraction and empirical potential structure refinement simulation. We find that the glass-forming abilities (GFA) of AY-bearing melts are intriguingly correlated with the dependence of melt structure on temperature. In the case of the Al2O3 and Y3Al5O12 (YAG), the observed large structural changes from superheating to undercooling melt (i.e., higher temperature susceptibility) correspond to a low GFA. Conversely, the 74Al2O3–26Y2O3 (AY26) melt, with the smallest temperature susceptibility, exhibits the highest GFA. Simulation models illustrate that the temperature susceptibility of melt is associated with its atomic arrangement, especially the stability of cation-cation pairs. A balanced network (in AY26 melt), where the unsteady OAl3 tri-clusters are minimized and steady apex-to-apex connections between adjacent network units are abundant, contributes to stabilizing cationic interactions. This, in turn, fosters the formation of large-sized Al-O-Al rings, which topologically facilitates the subsequent glass-forming transition. Our findings provide new structural insight into the GFA of AY-bearing melts and may expand to other unconventional glass-forming systems to accelerate glassy materials design.