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Since the Granger causality analysis was proposed, it has been constantly extended and widely used in engineering, signal processing and neural science and other fields. Because the Granger causality analysis has the advantages of containing the time information and without prior knowledge, it is gradually applied in the effective connectivity analysis of fMRI data in the field of effective network of the brain. Conditional Granger causality analysis can distinguish between direct causal influences from one region to another and indirect ones mediated through a third region. It makes the brain network structure more accurately. But if there are too many nodes in a brain network, it is lead to a large amount of calculation.In this paper, conditional Granger causality is used to analyze the effective connectivity of DMN of three groups:61neuroleptic-treated schizophrenia patients,22neuroleptic-naive schizophrenia patients and60healthy controls.We use the PCA based conditional Granger causality for reference, and proposed the method of using Bootstrap to test the significance of the conditional Granger causality value and using the binomial distribution test to extrapolate individual network to overall network. We put forward a completed method of constructing overall conditional Granger causality network to analyze the information transmission mechanism in the brain.In the overall network of medication patients with schizophrenia, we found Posterior Cigulate become a functional hub. In this paper, two sample T test was used to find the difference of topological properties between two networks. We found in the RMPF, healthy controls’shortest path is significant higher than schizophrenia patients. To study the association between the abnormal causal connection in the overall network and the symptoms of schizophrenia, correlation analysis was conduct between Granger causal connection and PANSS. The connection of RpH--->pCin was found correlating with many clinical symptoms. This may provide evidence for the diagnosis of schizophrenia.