The invention provides a three-dimensional coordinate model construction method of a software complex network, and belongs to the field of software complex networks. The method comprises the steps that firstly, target structured software is determined, a complete software source code is obtained, static scanning is performed on the target software source code, functions in software and a calling relation between the functions are analyzed, then, the functions are adopted as network nodes, the function calling relation is adopted as a network side, a function calling network is constructed, function calling sequence information is added into the function calling network, according to the function calling sequence information and the function calling topological structure, a set of unique three-dimensional coordinates are generated for each function node and written into the network nodes, the function calling coordinate network based on the function calling sequence of the structured software is obtained, and the three-dimensional coordinates are used for guiding network visualization work. The obtained network nodes are much orderly, and logic information related to software operation can be provided for the complex network model.