Abstract: The incompetent layers, as a key geological unit controlling structural deformation, is widely present in sedimentary basins. It is characterized by relatively low shear strength, hardness, and significant plastic flowability. These properties make it resistant to brittle failure under lateral compression while providing excellent sealing capacity, making it an ideal caprock for hydrocarbon accumulation. However, the widespread development of incompetent layers also complicates structural deformation patterns within basins.Based on the analysis of the mechanical properties of incompetent layers and the associated structural deformation evolution, this study selects a typical "platform-slope-platform" fault as a pre-existing fault structure. A comparative experiment is designed with and without a incompetent layers overlying the fault. Using finite element modeling, lateral compression conditions are applied to the two groups of models. By comparing the simulation results, the study systematically analyzes the role of the incompetent layers overlying the pre-existing fault in controlling structural deformation during tectonic processes and investigates the relationship between the thickness of the incompetent layers and the wavelength of the overlying folds.The results indicate the following: (1) The incompetent layers is a critical factor in inducing stratified deformation. Under lateral compression, the incompetent layers undergoes plastic flow accompanied by localized thickening and thinning, significantly absorbing the strain of the underlying structure. This results in a vertically decoupled deformation pattern above and below the incompetent layers; (2) The thickness of the incompetent layers is positively correlated with the wavelength of the overlying folds. A thicker incompetent layers leads to longer fold wavelengths, smaller amplitudes, broader horizontal extension, and more pronounced stratified deformation characteristics; (3) The incompetent layers plays a regulatory role in the deformation of the underlying structure. Its presence causes the underlying structure to exhibit a steeper deformation style, while the overlying structure displays relatively gentle fold patterns.