The invention provides an internal control system management method with a process structure as a core, which includes: constructing a process architecture, wherein the process architecture includes single or multiple architecture nodes, the architecture node is the business action after the management actions such as approval and approval are removed from the process of organization application,and each architecture node is composed of basic attribute, form attribute and risk attribute; when the process architecture is created successfully, copying the process architecture into different process templates according to different departments, so that different users can select the process templates to copy and form the proprietary process management; The process starts to flow automatically. After completing the work content of the node, whether to approve or not is judged according to the approval content of the process template node. The data of the architecture node is exchanged with the back-end by using no-refresh mechanism. The invention realizes the combination of process management and internal control management in software, realizes the management duplication quickly, andsimplifies the examination and approval process.