The microstructure evolution of GH4698 nickel-based superalloy was studied over a temperature range of 1000–1200 °C, a strain rate range of 0.01–1 s−1 and a strain range of 0.1–0.9 by uniaxial thermal compression. The dynamic recrystallization (DRX) behaviour and nucleation mechanism were characterized by electron backscattering diffraction (EBSD). Compared with the strain rate, the deformation temperature had a significantly different effect on the DRX volume fraction, DRX average grain size and grain boundary misorientation. Three types of DRX mechanisms may operate during thermal deformation. Discontinuous dynamic recrystallization (DDRX) characterized by serrated and bulging grain boundaries was the dominant DRX mechanism. Continuous dynamic recrystallization (CDRX) primarily occurred within the deformed grains, as well as at the interface between the dynamically recrystallized grains and the deformed matrix due to the difference in deformation compatibility in the original grains under various conditions. The pre-existing Σ3 twins can promote DRX nucleation through DDRX and twin dynamic recrystallization (TDRX) mechanisms. The verification of different DRX mechanisms is helpful to comprehensively understand the microstructure evolution of GH4698 nickel-based superalloys during thermal deformation.