In many business domain, flow diagrams play more and more important roles with which to represent commercial operation process. Many professional persons promote capability of decisions by means of this graphical descriptive tool. One of important issues is that given a diagram how to obtain the similar peer ones in repository or rank them according to designed algorithms. In this paper, we introduce a novel metric algorithm. Compared to previews methods, we focus not only on conventional semantic or syntactic similarity, but also on the nodes order in entire diagram hierarchical relationship. By precisely studying hundreds of diagrams, we conclude that node's layer order affect the similarity between two diagrams in some fields, such as business diagrams. We integrated layer order weight value and texts information embedded in the node into the flow diagram similarity measure system. Experimental results show that our algorithm is valid and efficient especially when considering layer orders.