The computational modeling of thin-walled structures based on isogeometric analysis (IGA), non-uniform rational B-splines (NURBS), and Kirchhoff–Love (KL) shell formulations has attracted significant research attention in recent years. While these methods offer numerous benefits over the traditional finite element approach, including exact representation of the geometry, naturally satisfied high-order continuity within each NURBS patch, and computationally efficient rotation-free formulations, they also present a number of challenges in modeling real-world engineering structures of considerable complexity. Specifically, these NURBS-based engineering models are usually comprised of numerous patches, with discontinuous derivatives, non-conforming discretizations, and non-watertight connections at their interfaces. Moreover, the analysis of such structures often requires the full stress and strain tensors (i.e., including the transverse normal and shear components) for subsequent failure analysis and remaining life prediction. Despite the efficiency provided by the KL shell, the formulation cannot accurately predict the response in the transverse directions due to its kinematic assumptions. In this work, a penalty-based formulation for the blended coupling of KL and continuum shells is presented. The proposed approach embraces both the computational efficiency of KL shells and the availability of the full-scale stress/strain tensors of continuum shells where needed by modeling critical structural components using continuum shells and other components using KL shells. The proposed method enforces the displacement and rotational continuities in a variational manner and is applicable to non-conforming and non-smooth interfaces. The efficacy of the developed method is demonstrated through a number of benchmark studies with a variety of analysis configurations, including linear and nonlinear analyses, matching and non-matching discretizations, and isotropic and composite materials. Finally, an aircraft horizontal stabilizer is considered to demonstrate the applicability of the proposed blended shells to real-world engineering structures of significant complexity.