Accurate and complete diagnosis of nuclear accidents is the primary link to nuclear emergencies. The signed directed graph (SDG), as a common method of fault diagnosis, has good completeness. However, if there are feedforward and negative feedback control loops, compensation response and reverse response will be generated in the process of fault occurrence and propagation, which makes the state of the compensation variable and reverse variable uncertain, thus destroying the compatibility of the fault propagation path, leading to incomplete SDG reverse reasoning. In order to solve this problem, this paper proposes a SDG fault diagnosis method based on information flow. This method first finds out all the directed edges with the compensation variable or inverse variable node as the endpoint. By comparing the goodness of fit between the information flow on these directed edges and their total information flow curves, the path that contained the directed edge represented by sub-information flow with the highest R2 is obtained, and it is used as the fault propagation path with the maximum probability to determine the state of the compensation variable or inverse variable and fault location. At the same time, this paper extends the SDG model from the structure to build an FR-SDG model that can intuitively describe the node steady-state information under the final response and the fault propagation path with the maximum probability, which improves the diagnosis resolution. Finally, this paper carried out the relevant experiments in the subsystem of the nuclear reactor primary loop by using the simulation system PCTran AP1000, which verified the feasibility of this method.