Three relatively novel initial microstructures of Mg–Gd–Y–Zn–Zr alloy were regulated by heat treatment, the deformation behavior of long period stacking ordered (LPSO) phases with different morphology and distribution and their role on recrystallization during thermal deformation were systematically investigated. The interdendritic block-shaped LPSO phases exhibit higher deformation resistance, and shearing, bending, kinking, tearing, dissolution, together with the breaking of plate-shaped lamellae produced by dissolution, are the main deformation mechanisms for them to coordinate deformation. As for the lamellar LPSO phases, deformation behaviors such as shearing, bending, kinking and breaking mainly occur. The interdendritic block-shaped LPSO promote recrystallization through the particle-stimulated nucleation (PSN) mechanism, and the PSN effect is enhanced with the increasing phase fraction, also, the broken block-shaped LPSO have better PSN effect. Recrystallized grains tend to nucleate at the kink of lamellar LPSO and form recrystallized grains bands along the kink bands; the fragmented fine lamellae have better PSN effect, promoting numerous recrystallization nucleation in the severely deformation zone, meanwhile, the joint pinning effect of the fragmented lamellae and precipitates β-phase results in the smaller recrystallized grains size. However, the intragranular continuous large-sized lamellar LPSO strongly pin the dislocation movement and hinder migration of recrystallized grain boundaries along the basal plane and c-axis of lamellar LPSO, making it difficult to achieve extensive lattice rotation, which is not conducive to the recrystallization nucleation. The most remarkable work in this paper is that we clarified the mechanism of different LPSO phases, especially lamellar LPSO phase, on recrystallization behavior, and these findings will provide microstructure regulation guidance for thermal-deformed Mg–Gd–Y–Zn–Zr alloys containing LPSO.