This study aims to explore the effect of deformation parameters on microstructure evolution during the new two-stage annealing method composed of an aging treatment (AT) and a cooling recrystallization annealing treatment (CRT). Firstly, the hot compressive tests with diverse deformation parameters were finished for an initial aged deformed GH4169 superalloy. Then, the same two-stage annealing method was designed and carried out for the deformed samples. The results show that the deformation parameters mainly affect the grain microstructure during CRT by influencing the content, distribution and morphology of the δ phase after deformation. The reason for this is that there is an equilibrium of the content of the δ phase and Nb atom. When the deformation temperature is high, the complete dissolution behavior of the δ phase nuclei promotes the dispersion distribution of the δ phase with rodlike and needle-like shapes during AT. Thus, the fine and heterogeneous microstructure is obtained after annealing because the recrystallization nucleation is enhanced in those dispersed δ phases during CRT. However, when the retained content of δ phase nuclei is high after deformation, the clusters of intragranular δ phases will form during AT, resulting in the pinning of the motion for dislocation. The elimination of the mixed grain microstructure is slowed down due to the low static recrystallization (SRX) nucleation rate within the deformed grain.