Structural health monitoring (SHM) is a technology that is used to improve the safety, stability, and availability of large engineering structures. One important aspect of SHM is the ability to perform real-time reconstruction of the full-field structural displacements, also known as shape sensing. The inverse Finite Element Method (iFEM) is a technique that has been used for three-dimensional shape sensing of structures using strain data. On the other hand, Isogeometric Analysis (IGA) is a method that utilizes smooth spaces of functions, such as non-uniform rational B-splines, to solve structural problems and has gained significant attention in recent times. In this study, the authors propose a new method for shape sensing of complex stiffened shell structures by combining IGA with the iFEM method. The goal of this research is to accurately reconstruct the complex geometry of the structure without the need for a fine numerical discretization or mesh. To achieve this, the authors have developed an isogeometric Mindlin-Reissner inverse-shell element (IgaiMin) to implement the coupling between IGA and iFEM. The proposed method is validated by solving problems involving simple plates, tee junctions, and partly clamped stiffened panels representing ship structures.