The 18R-type long-period stacking ordered (LPSO) structure in Mg85Zn6Y9 exhibits phase transition into D03 and α-Mg (D03/α-Mg) before it transforms into a liquid phase with the increase in temperature at 7.8 GPa. First-principles calculations suggest that the energy barrier between 18R-type LPSO and D03/α-Mg decreases with pressure. A further increase in the temperature decreases the energy difference between LPSO and D03/α-Mg. Therefore, the free energy variations due to the effects of both pressure and temperature cause phase transition. The D03/α-Mg phases formed at high pressure can be recovered at 0.1 MPa and room temperature. The phase transition from 18R-type LPSO structure to D03/α-Mg causes inner-grain diffusion and generates a lamellar structure. The thickness of the lamellar structure decreases with the increasing pressure until it reaches 65 nm at 15 GPa. Moreover, the alloy solidified above 5 GPa also comprises D03/α-Mg phases. The alloy solidified at 5 GPa exhibits a typical eutectic lamellar structure. However, spherulite-like polycrystalline microstructures containing ultrafine grains are obtained when the alloys are solidified at 10 and 15 GPa. The microstructure variations are caused by an increase in the degree of supercooling due to atomic diffusion suppression with the increasing pressure. The alloys containing D03/α-Mg exhibit both low modulus and ultrahigh strength. The Young’s modulus is related to the presence of the D03 and α-Mg phases in the alloy structure. In contrast, the increase in σy can be attributed to the grain refinement strengthening.