The identification of soil heaves inside a caisson during installation is important for the caisson's design length, since the inner soil heave during the caisson installation affects the final effective caisson penetration depth, hence caisson capacity. This paper reports an extensive parametric study of stiffened caissons penetrating in double-layer of soft-over-stiff clay using large deformation finite element (LDFE) analyses. The LDFE analysis was first validated against the existing results from centrifuge tests and numerical analyses. Then the parametric study was carried out to explore the inner soil movements during stiffened caisson installations with various influencing factors, such as caisson diameter, caisson stiffener width, top-layer soil strength, double-layer soil strength ratio, and roughness of soil-caisson interface. It is found that the caisson diameter, stiffener width, and top-layer soil strength have significant influences on the inner soil behaviors. Besides, the movements of both soil surface and soil layer interface were also investigated. Based on the LDFE results, design formulas are proposed to estimate the inner soil heaves for soft-over-stiff clay. A design formula to estimate the movement of the soil layer interface for soft-over-stiff clays is also reported.