Abstract Lithium disilicate glasses and glass–ceramics are good potential candidates for biomedical applications, solid‐state batteries, and serve as models of nucleation and crystal growth. Moreover, these glasses exhibit a phase separation that influences their nucleation and crystallization behavior. The atomistic mechanisms of the phase separation and their pressure dependence are unclear so far. Here, we used molecular dynamics simulations supported by experiments to assess the spatial heterogeneity of lithium disilicate glasses prepared under pressure. We show that the glass heterogeneity decreases with increasing the pressure under which the system was cooled and almost disappears at pressures around 30 GPa. The origin of the heterogeneity is due to the attraction between Li cations to form clustering channels, which decreases with pressure. Through our results, we hope to provide valuable insights and guidance for making glass–ceramics with controlled crystallization.