The Ni-Fe-based superalloy GH4169 (Inconel718) is widely used for several critical gas-turbine components which are hot forged. Its microstructure and property are sensitive to the parameter adjustment during hot working process. To obtain required low-cycle fatigue and fracture properties, it is essential that the microstructure is controlled during preheating and heat treatment. The evolution of non-uniform microstructure during hot working is more complicated than that of uniform microstructure. On the other hand, various secondary phases can be observed in GH4169 alloy, thus it is important to investigate the effect of secondary phases on the microstructure evolution during forging process. In this work, the mechanisms of non-uniform microstructure evolution in GH4169 alloy were studied by analyzing the evolution of secondary phases, grain boundary misorientation, grain size and interactions of dislocation. It is found that the volume fraction of δ phase increases with the increasing of temperature and heating time at the lower temperature. While at the higher temperature, it decreases monotonously with the temperature increasing, but increases first and then decreases to stable value with time increasing. The pinning effect of secondary phases in GH4169 alloy can be concluded that the γ" phase and δ phase precipitated within the grains retain movement of dislocation, the δ phase precipitated at the grain boundary hinders the nucleation and growth of recrystallized grains, and the carbides limits the grain growth. The frequency of low angle grain boundary decreases with temperature and time increasing, and the mobility of low angle grain boundary increases with temperature increasing. The uniformity of microstructure and the size of equaxied subgrain increases with heating temperature and time increasing. Continuous recrystallization of elongated grain occurs at specific conditions. The mechanisms of non-uniform microstructure evolution during heating process can be concluded as subgrain growth, recrystallized grain growth, and anneal twinning nucleation and growth. The recrystallized grains are formed by the growth of subgrains conducted by the rotation of low angle grain boundary and the movement of dislocation. When the grain growth is pinned, the mechanisms for the energy dissipation is the nucleation and growth of anneal twinning. And the growth of anneal twinning promotes the generation of low angle grain boundaries at the tip of partial anneal twinning.