<p>A novel isogeometric/super-ellipsoid discrete element coupling method (IGA-SEDEM) is proposed to model contact interactions between structures and complex shaped particles. This coupling approach adopts the super-ellipsoid discrete element method for particles with high geometric flexibility. The isogeometric analysis (IGA) framework is employed for continuous solids, leveraging its exact geometric representation of computer-aided design models to enhance contact force accuracy and ensure time-stepping stability. In the global search stage, the CGRID method is enhanced through a support point algorithm to efficiently detect potential contact pairs between super-ellipsoid particles and IGA surfaces. The local search stage resolves exact contact points and penetrations between super-ellipsoid particles and IGA surfaces. To achieve this purpose, the simplex method and Brent’s algorithm are augmented with a support point approach to solve non-linear contact equations. Subsequently, contact forces are computed via a penalty-based model, where the stiffness parameters are adaptively scaled based on the local curvature of super-ellipsoid surfaces to avoid overshooting. Furthermore, a support point iteration algorithm is proposed for contact point detection between convex super-ellipsoid particles. The accuracy of the coupling method is validated against a benchmark based on the finite element method, where a rigid super-ellipsoid particle impacts a quarter-cylinder structure, achieving substantial congruence. Two additional examples—a corrugated plate impacted by 1135 super-ellipsoid particles and a basin subjected to 11,466 super-ellipsoid particles—demonstrate the robustness and applicability of the proposed coupling method in handling large-scale granular systems.</p>