Nickel-based single crystal superalloys are critical materials for manufacturing advanced aircraft engine blades. During operation, microstructural changes in alloys under the applied stress significantly influence their fatigue and creep performances. However, relying solely on experimental methods poses challenges in capturing the dynamic processes by which the applied stress affects the alloy microstructure. Utilizing computational simulations to study the impact of the applied stress on the rafted γ' phase in single crystal superalloys offers distinct advantages. In this study, specific slip systems activated within the γ matrix are identified based on the type of the applied stress and their intrinsic plastic strain is calculated. The simulation models the formation of rafting under the applied stress and investigates the evolution of the microstructure during the rafting process in nickel-based single crystal superalloys. This study focuses on the effect of plastic strain within γ channels on the formation of the rafting morphology during the early stages of creep formation. Plastic strain generated under externally applied tensile stress promotes the preferential growth of γ′ precipitates along specific directions, which is the primary cause of γ′ phase rafting. Moreover, the lattice misfit directly determines the type of rafting (N-type or P-type). The spacing of dislocations at the γ′/γ interfaces, such as along {001} planes, significantly affects the morphology (aspect ratio) of γ′ precipitates but does not influence the growth kinetics or volume of γ′ precipitates at a given time step. In contrast to tensile stress, shear stress induces rafting microstructure coarsening at angles of approximately 30° or 60° relative to the horizontal direction, closely associated with activated slip systems. Additionally, different combinations of slip systems can result in the distortion of γ channels.