To realize the fault diagnosis of complex systems, a fault diagnosis method for complex systems based on the explanatory structural model is proposed. According to the fault mechanism analysis, the fault association matrix of system elements is established. The explanatory structural model is applied to transform the fault association relationship of complex systems into an intuitive hierarchical structural model through matrix transformation, so as to realize the structuring and hierarchical propagation of system faults. The PageRank algorithm is introduced to evaluate the influence and impact of system element faults. According to the influence and impact of the same-layer components and the fault transmission logic, the main cause of system fault transmission is clarified, which provides a basis for fault diagnosis. Finally, a specific application is carried out with a certain device as an example to verify the effectiveness of the method.