A new fault diagnosis method based on multi-signal flow graph (MSFG) has been proposed to deal with online complex system diagnosis. This method has three steps. The first step is to develop a multi-signal graph model for the object system and generate a dependency matrix as diagnostic knowledge. The second step is to generate conflict sets by the dependency matrix and the system observation vector, and then the problem of finding the minimal diagnosis set is transformed into a problem of integer programming. In the final step, the optimal solution of the problem of integer programming is calculated by using a branch-and-bound algorithm for diagnosis. In this way, explosion problem caused by enumeration can be avoided. In order to facilitate the application of MSFG modeling and on-line diagnosis in real problems, an Intelligent Diagnostic Platform (IDP) that provides a MSFG modeling environment and employs the branch-and-bound algorithm for Complex System diagnosis is developed. The structure of the software IDP is presented. Finally, a case study for a fuel system of aircraft is described in detail to illustrate the procedure of using IDP for diagnostic problems and to demonstrate the effectiveness of the proposed method.