Intelligent mechanical systems are a focused area nowadays. One of the requirements of intelligent mechanical systems is to achieve intelligent fault diagnosis through the real-time acquisition and analysis of data from various sensors installed on mechanical components. In this paper, a new fault diagnosis method is proposed to solve the problems of difficulty in integrating the fault diagnosis algorithm and locating fault parts due to the complexity of modern mechanical systems. The complexity of modern industrial intelligent systems is due to the fact that the systems are composed of multiple components and there are various connections between them. Common fault diagnosis is to design specialized fault identification algorithms for the physical characteristics of each component, and the integration of different algorithms is a major challenge for system performance. Therefore, this paper investigates a general algorithm for the fault diagnosis of complex systems using the timing characteristics of sensors and transfer entropy. The fault diagnosis algorithm is based on the prediction of multi-dimensional long time series using Autoformer, and fault identification is performed based on the deviation of the predicted value from the actual value. After fault identification, a root cause analysis method of faults based on transfer entropy is proposed. The method can locate the component where the fault occurs more accurately based on the analysis of the cause–effect relationship of each component and help maintenance personnel to troubleshoot the fault.