In order to compare the reliability of different functional brain network which were be constructed by different function connection definition methods, the discrepancy between different function connection definition methods of network were studied through the proposed method that calculate the inherent network index from the node properties’ perspective. This method can make up for the inadequacy of traditional comparison methods that ignore the network structural characteristics. Experimental results show that this method can effectively measure the pros and cons of network connection definition. The experimental results also indicate that for the reliability of edges in function brain network constructed by different connection definition methods, Pearson correlation method is better than wavelet correlation method and partial correlation method is worse than wavelet correlation method.