Oxide glasses are generally formed by a network of glass former polyhedra, and network modifiers having the role, either to neutralize/ stabilize the charge of the glass former polyhedra or depolymerize the glass network. The effect of the modifier content on the structure and properties of the glass are to some extent, well known. However, the effect of the type of modifiers on the clustering and the tendency to form a phase separation in the glass is not investigated in detail and still not fully understood until now. Here, we use molecular dynamics to investigate the effect of the modifier type on the structure and the clustering tendency of a series of modified silicate glasses. Specifically, we show that the tendency of modifier—modifier cluster formation is linked to the modifier size and modifier—oxygen bond strength. The effect of different modifiers on the short- and medium-range structure of the glass is also discussed. This allows us to get an overview of the effect of cations nature on the properties of the glass and opens a new window for further development and optimization of the glass properties.