With the problem of inter-industry linkage, based on the theory of complex networks, this paper takes the input-output flow table of Yunnan Province for example, and analysis the relationships of 42 sectors of industry. Firstly, at the threshold level of 0.1%, drawing the network of industrial structure. There is complex relationship between industry departments by the graphs .Secondly, using the factions filtering algorithm analyses the industrial agglomeration of Yunnan Province, it showed four communities and the connection between these within the industry became more closely by the average path length, clustering coefficient, etc. statistics.