As nickel-based alloys are more and more widely used in engineering fields for bearing cyclic loadings, it is necessary to study their very-high-cycle fatigue (VHCF) properties. In this paper, the fatigue properties of nickel-based alloy 625 were investigated using an ultrasonic fatigue test apparatus. The fracture microscopy shows that around the crack initiation site there are two characteristic zones, a rough area (RA) and a fine granular area (FGA). Inclusions caused the interior fatigue crack initiation, and the coalescence of neighboring micro cracks was strongly influenced by the local microstructure, resulting in the RA morphology. Subsequently, the contact and compressing of the crack surfaces contributed to the formation of the FGA. Finally, the stress intensity factors of the RA and FGA were quantitatively evaluated for further discussion of the crack initiation and propagation processes.