The increasing electrification and integration of advanced controls in modern aircraft designs have significantly raised the number and complexity of installed printed circuit boards (PCBs), posing new challenges for efficient maintenance and rapid failure detection. Despite self-diagnostic features in current avionics systems, circuit damage and multiple simultaneous failures may arise, compromising safety and diagnostic accuracy. To address these challenges, this paper aims to develop a fast, accurate, and non-destructive, multi-failure diagnosis algorithm for PCBs. The proposed method combines a self-attention mechanism with an adaptive graph convolutional neural network to enhance diagnostic precision. A convolutional neural network with residual connections extracts features from scalar magnetic field data, ensuring robust input diversity. The model was tested on a typical dual-phase amplitude boosting circuit with up to four different simultaneous failures, achieving the experimental results of 99.08%, 98.50%, 98.78%, 98.01%, 98.93%, 98.25%, 97.03%, and 99.77% across metrics including overall precision, per-class precision, overall recall, per-class recall, overall F1 measure, and per-class F1 measure. The results demonstrated its effectiveness and feasibility in diagnosing complex PCBs with multiple failures, indicating the algorithm’s potential to improve failure diagnosis performance and offer a promising PCB diagnosis solution in aerospace applications.