GH4706 Ni-based superalloy is widely used for aero-engine turbine disks operating below 700 °C, where high-temperature ductility is critical to avoid cracking during die forging and service. However, the microscopic mechanisms by which stabilization treatment regulates its high-temperature ductility remain insufficiently clarified. This study systematically investigated the tensile deformation behavior at a high temperature of 650 °C of the GH4706 Ni-based superalloy after stabilization treatment. Transmission electron microscopy (TEM) and secondary ion mass spectrometry (SIMS) were employed to characterize microstructural evolution and elemental redistribution to clarify the microscopic mechanisms by which stabilization treatment enhanced the high-temperature ductility of the GH4706 alloy. The experimental results indicated that better high-temperature plasticity was obtained, although tensile strength decreased slightly after stabilization. This improvement was mainly attributed to the precipitation of the η phase (Ni₃Ti) and its synergistic interaction with the matrix, which effectively enhanced the plastic deformation capacity of the GH4706 alloy at elevated temperatures. Moreover, η phase precipitation and elemental segregation enhanced grain boundary stability, thus inhibiting crack initiation and delaying necking. SIMS analysis revealed that boron, phosphorus, and sulfur showed significant segregation along grain boundaries during 650 °C tensile testing following stabilization—an effect considered crucial to the observed ductility enhancement. TEM observations further indicated that the interaction between η phase precipitation and the nucleation and evolution of stacking faults during deformation together reduced local stress concentrations and promoted uniform plastic deformation.