In this work, the annihilation mechanism of stacking faults (SFs) in epitaxial 3C-SiC layers grown on Si(001) substrates is studied by molecular dynamics (MD) simulations. The evolution of SFs located in the crossing (11) and (11) glide planes is considered. This evolution is determined by the interaction of 30° leading partial dislocations (PDs) limiting the stacking faults under the slightly compressive (∼0.45%) strain condition during the 3C-SiC layer growth. It is characterized in key terms: the distance between the PDs and the mutual orientation of their Burgers vectors. Two SF annihilation scenarios are revealed. In the first scenario, two PDs with opposite screw components of Burgers vectors, leading the SFs located in the (11) and (11) planes, are close enough (∼15 nm or less) and attract each other. As a result, the propagation of both SFs is suppressed via the formation of a Lomer–Cottrell lock at their intersection. In the second scenario, two PDs are far away one from the other (beyond ∼15 nm) and do not interact, or they repulse each other having equal screw components of their Burgers vectors. In this case, the propagation of only one of the SFs is suppressed. Obtained results explain the mechanism of SF annihilation and formation of SF intersection patterns experimentally observed by TEM investigations. They will provide important implications for the elaboration of advanced methods for the reduction of SF concentrations in epitaxial 3C-SiC layers on Si substrates.