<p>This paper provides insight into the inner soil behaviour of stiffened caisson penetration in stiff-over-soft clay that is a common soil profile for the application of caissons. Large deformation finite element (LDFE) analyses were conducted to simulate the installation process of stiffened caisson from the seabed surface with jacking process. Soil-flow mechanism and inner soil heaving were analysed. After the validation of LDFE method, an extensive parametric study was performed, investigating the effects of caisson geometry and layered soil strength profile (including the normalized strength of the top soil layer, soil strength ratio, and the thickness of the top layer). The results showed that three soil-flow mechanisms could occur during stiffened caisson installation in stiff-over-soft clays: Mechanism I—surcharge mechanisms; Mechanism II—trapped mechanism; and Mechanism III—plugging mechanism. Based on the three mechanisms identified, a design framework for assessing inner soil heaves was established to provide guidance for caisson foundations.</p>