The low cycle fatigue behaviours of a microstructure rafting Ni-based single crystal superalloy have been experimentally investigated at 980 ℃. Deformation of γ/γ’ phases and the corresponding dislocation configurations were investigated, highlighting rafting γ/γ’ morphology that contributes to crack initiation and propagation, as well as macro-scale accumulated plastic strain. Unlike the discrete slip lines of a virgin superalloy, intense slips developed along the parallel {111} slip plane result in crossed slip bands in the rafting superalloy. The decreased resistance of widened γ channels to dislocation movement, along with the prevention of dislocation cutting through γ’ precipitates in pre-existing dense dislocation networks, facilitates crack propagation in the γ channel in the slightly rafting superalloy. As the rafting state increases, the dislocation network loses its protective effect by reducing coherency stress and acting as a superdislocation source, which facilitates crack propagation along the γ/γ’ interface. Finally, a microstructure-based fatigue model is developed considering the reduction of deformation resistance induced by rafting. The fatigue loading control mode effect is introduced by a combination of resolved shear stress and tensile stress effects on crack initiation. The LCF life of rafting Ni-based superalloys significantly decreases under stress-controlled conditions compared to strain-controlled conditions due to the increase in cumulative plastic strain. However, the insignificant impact of the initial surface oxide layer on LCF life is revealed.