With the increase of aircraft service time and the extreme service environment, fatigue cracks and other defects may occur in the multi-layer metal riveting structure of aircraft. It is of great significance for damage assessment and maintenance to find defects in time and obtain information such as defect depth and direction. However, due to the concealment of defects caused by multi-layer structure, the detection signal characteristics of conventional eddy current probes are indistinct, and conventional eddy current probes are not sensitive to defects in certain directions, making it difficult to determine the direction of fatigue cracks. To address these problems, a cross-runway-type differential eddy current probe is designed, which is mainly composed of a cross-runway-type excitation coil and two sets of differential detection coils. The feasibility of the new eddy current probe is investigated by establishing a three-dimensional finite element model for defect detection of aircraft multi-layer metal riveting structures, including the optimization of the structure of the probe, and simulations are conducted to analyze the different directions of defects, the buried depths and the lift-off heights, respectively. The results indicate that the new probe can effectively detect deep defects with a buried depth of 6 mm and dimensions of 10 mm×1 mm×1 mm, and it can obtain the direction information of the defects. Compared to traditional probes, designed probes have advantages such as no missing defects in all directions, resistance to lift off effects, and high resolution. The research results can provide some reference for the design of eddy current probes for aircraft multi-layer metal riveting structure detection.