Hostile environmental pressure on supply chain management increases emphasis on supply chain agility, integration, and visibility to respond rapidly, effectively and efficiently to changes in the marketplace. There is a need for new methods and tools to visualize the supply chain topologies which captures and recognizes the complexity of the supply chain network. This paper presents a Knowledge-based Customization System for Supply Chain Integration (KCSSI) which is developed based on three core technologies: visualization of topologies, network analysis, and knowledge-based system so as to obtain quantified actionable information and formulating strategies for supply chain configuration leading the long term success. The performance of the system is verified by a series of controlled simulation experiments conducted in a selected reference site. It is verified that the KCSSI improves supply chain visibility by recognizing the structure clustering and interconnection of the supply chain network, quantifying and exploiting holistic supply chain performance to provide measurable insights for the customization of the supply chain configuration leading to long term success