Fully utilizing the post-buckling capacity of stiffened composite panels is important to reduce the weight of aeronautical composite structures. However, owing to the complex post-buckling failure modes and mechanisms, there are no effective analysis methods. This paper explores the impacts of the mode III fracture energy on the damage behavior of the stiffener–skin interface of composite stiffened panels under post-buckling conditions. To characterize the bonding interface damage, an interface damage initiation criterion considering the effects of through-thickness compression on the shear failure was used and combined with the Reeder damage extension criterion, which considers the mode III fracture. The mode III fracture toughness characteristics of the damage evolution of the stiffener–skin interface were obtained using the edge crack torsion (ECT) test method. Moreover, the compressive deformation response, buckling load, buckling modes, failure load, and failure modes of the panel were obtained by a compression test of I-shaped stiffened panels. Based on the aforementioned experimental data and numerical model, the post-buckling behavior of the I-shaped stiffened composite panels with an open cross-section stiffener was studied. It was found that the mode III fracture energy caused by the longitudinal shear stress τ31 played a major role in the stiffener–skin interface damage extension of the stiffened panels. Therefore, the mode III fracture behavior should not be ignored in the post-buckling analysis. The numerical analysis method developed can accurately predict the damage initiation and evolution processes of the composite panel interface. The method can be effectively used for post-buckling analysis of aeronautical composite panels.