Multi-layered aeronautical structures, such as fuselage panels and wings, are composed of several layers of materials such as metal and composites. These structures are prone to damage such as corrosion, cracks and delamination between layers, which can compromise their structural integrity. Eddy current sensors are an essential tool for the inspection and preventive maintenance of multi-layered aeronautical structures, contributing to the safety and reliability of these crucial components. Differential-mode eddy current sensors are particularly well-suited for the inspection of multi-layer aerospace structures around dished-head rivets. The differential measurement improves the detection and characterization of defects in these complex geometries, which are prone to fatigue, corrosion, and other types of damage. The advantages of differential mode are improved sensitivity to small defects, elimination of lift-off variations (distance between the sensor and the surface), reduced electromagnetic interference and detection of defects around rivets, which are critical and difficult to access areas. This work deals with a study of the rotational differential sensor signal according to geometrical parameters of fastener holes defect. It is carried out by an eddy current nondestructive testing system implemented under COMSOL Multiphysics. Indeed, despite its rapidity, the results have shown that the sensor is sensitive to the hole defects when the distances Sensor/Rivet and Lift-off are reduced. As predicted, the experimental results have shown the presence of unsuitable signals caused by the additional Lift-off and the distance Sensor/Rivet. As a solution, these tow parameters should be reduced and kept constant in order to get a better defect signal.