Advanced materials are widely used in many industries. They play an important role especially in the aeronautic and automotive sectors where weight reduction is required in order to reduce fuel consumption. Composite materials have a high strength to weight ratio and are applied in airplane construction. Nevertheless, sometimes it is not viable to replace all metal parts by composite ones due to the cost factor. In this sense, hybrid structures are highly welcome. In order to ensure the safety of these hybrid components during their entire life cycle, non-destructive testing evaluation (NDT&E) methods are used and sometimes they are the only option. In this study, we use infrared thermography (IRT) to inspect an aluminum-composite hybrid structure with a 3D shape. The sample has a composite part with a small metal inlay (EN AW-6082) overmolded with a thermoplastic layer. The inlay is bended to reach the desired 3D geometry. This sample was design to be used for the connection between an A- or B-pillar and a car roof made of carbon fiber reinforced polymer (CFRP). A dual-band infrared camera is used in order to capture images in two different spectral ranges. In addition, two data processing techniques for infrared images are applied to enhance the images: principal component thermography (PCT) and partial least squares thermography (PLST). Then, a signal-to-noise ratio analysis is performed with three randomly chosen previous known defects to assess the quality of the images and detected defects. Results showed that principal component thermography has a slight advantage over partial least squares thermography in our specific experiments. Specifically, for the long-wave infrared band, PCT presented, among the defects analyzed, PCT presented a mean value 12.5% higher while the standard deviation was almost three times lower than PLST. In parallel to the non-detructive analysis, a numerical finite element model was formulated in ANSYS® to analyze the total deformations to which the metal-composite-hybrid structure is subjected during a possible use. Results obtained with the numerical model indicate that the interface region between composite and metal parts is where the highest degree of deformation occur, which indicates possible regions where defects and failures may occur in real use cases.