The Mg–Zn–Y alloys show a good mechanical strength which can be achieved with the precipitation hardening by intermediate phases (X, W and I phase) in Mg solid solution (α phase). However, an accurate control of the microstructure formation is required in order to obtain good mechanical properties. In this study, experimental observations of microstructures of the Mg–Zn–Y system have been performed. Then we have focused on developing CALPHAD (CALculation of PHAse Diagrams) thermodynamic database to obtain the Gibbs free energy to draw phase diagram of the system and to understand the precipitation behavior of the intermediate phases. In order to understand the formation of microstructures, we have performed simulations of solidification of the alloy with use of multi-phase-field method. At the beginning the solidification process has been calculated for a large area, then the zoomed in region of the lamellar structures of the α phase and the W phase have been analyzed. Resulting optimum lamellar spacing reproduce experimental one well.