This study presents a stability analysis procedure for caisson structures and a case study for a honeycomb slit-caisson. CADMAS-SURF was used to calculate the wave pressures based on an irregular wave with a 50-year period and the data for three regular waves obtained from a target site. Then, the irregular and regular wave pressures were used to obtain the dynamic responses (stresses) of the caisson structure using an explicit time integration program, ANSYS/LS-DYNA. Finally, the DNV code was used for structural and fatigue stability analyses.