Wire arc additive manufacturing (WAAM) offers a scalable route for fabricating lightweight structures made by magnesium-rare earth (Mg-RE) alloys. However, intrinsic heat treatment (IHT) caused by thermal cycling poses critical challenges to achieving uniform microstructure and isotropic mechanical performance. Here, we elucidate the in-situ phase transformation behavior of long-period stacking ordered (LPSO) phases in WAAM-deposited Mg-7Gd-3Y-1Zn-0.5Zr (VWZ731K, wt.%) alloy thin wall. By employing multiscale characterization, thermodynamic simulations, and mechanical testing, we correlate thermal cycling history with microstructural evolution across the building direction. Due to prolonged exposure to thermal cycling, the Bottom region of VWZ731K thin wall experiences a reduction in stacking fault energy, which promotes the in-situ phase transformation of eutectic (Mg,Zn)₃(Gd,Y)→18R-LPSO. The presence of blocky 18R-LPSO phases enhances yield strength, however, crack propagation along the LPSO structures leads to a reduction in ductility. In contrast, the Top region predominantly forms needle-like γ′ phases, which, although associated with a lower yield strength compared to the Bottom region, contribute to improved elongation. This study provides mechanistic insights into IHT-driven heterogeneity in microstructure and mechanical property of WAAM-deposited Mg-RE alloys.