In this study, effect and mechanism of different stacking structures of LPSO phase on microstructures and mechanical properties of Mg-2.0Zn-0.3Zr-5.8Y under different extrusion temperatures were studied. The results showed that the average grain size of the alloy containing 18R and 14H LPSO phases reached 9.5±3.0μm under the extrusion temperature of 390℃, and the tensile strength and elongation reached 280MPa and 18.7%, respectively. When the extrusion temperature increased to 420℃, the 18R LPSO phase transformed to 14H structure, the grain size was refined significantly, and the tensile strength and elongation increased to 330MPa and 20.8%, respectively. With the increasing of extrusion temperature (over 420℃), the grain size increased and the tensile strength and elongation decreased. The variation of texture intensity under different deformation temperatures, the transformation of stacking structure and shape of LPSO phase and grain refinement are the main reasons caused the variation of mechanical properties of extruded alloy.