Silicate glasses have evolved from basic structural materials to enabling materials for advanced applications. In this article, we unravel the origin of the mixed alkali effect for alkali silicate 22.7R₂O–77.3SiO₂ glasses (R = Na and/or K) by identifying the variation in the alkali ion location around the non-bridging oxygen atoms. To do so, we constructed a state-of-the art structural model, which reproduces both diffraction and NMR data with a particular focus on the behavior of the alkali ions. A novel topological analysis using persistent homology found that sodium-potassium silicate glass shows a significant reduction in large cavities as a result of the mixed alkali effect. Furthermore, a highly correlated pair arrangement between sodium and potassium ions around non-bridging oxygen atoms was identified. The potassium ions can be trapped in K–O polyhedra due to the increased bridging oxygen coordination; therefore, the correlated pair arrangement is likely the intrinsic origin of the mixed alkali effect.