In the modern complex system, due to the gradual increase of system complexity, undecidable causal relation will appear with it. So it is hard for a model to satisfy all causality perfect conditions. When processing imperfect causality model, the system is considered as not diagnosable in the diagnostic result of the above method, that is to say, the related diagnostic result cannot be provided. Therefore, based on the existed imperfect local solution method, this paper propose a kind of dealing with the problem in which the overall situation cannot be diagnosed because of causality deletion in intelligent fault diagnosis hybrid system. Automation chain is generated through decomposed temporal causal graph and local diagnosis is done within automation chain. When model causality is perfect, provide perfect diagnosis result. When causality is imperfect, local maximum diagnosis result is provided. The test result shows that this method can effectively solve a series of similar diagnosis problems of hybrid system.