The Logistics Service Provider (LSP) industries are undergoing radical change. Not long age, LSP was understood to be responsible for the delivery of goods from producer to customer. Nowadays, however, the emphasis is much more on the organization and management of the entire logistics supply chain between manufacturers, warehouses, distributors, and the end-customers of subsequent stages. The logistics operations integrate with the information technology having become a trend owing to the complexity of logistics and the rapid development of information technology. To the logistics industry, how to use information technology well to delivery products to the customers with the right quantities at right time becomes a critical issue. How to get the accurate information to improve the utilization of manpower, capital and resources of the whole industry is also the tough issue to LSP. The proposed methodology of this research is to develop a Business Process-Oriented Methodology for Designing Information System of Distribution Center. Briefly speaking, this system is adopted Systems Life Cycle Design (SDLC) methodologies in the software specification and creation processes. We also apply the concepts of Quality Function Deployment (QFD) and Business Process Management (BPM) techniques, including Enterprise Ontology and Unified Modeling Language (UML), to define system requirements and specifications. Our proposed methodology can provide the functions as follows: (1) Integrating physical logistics processes and information system processes to improve the efficiency, (2) Containing the capacity to be flexible in order to meet the needs of both system users and customers, and (3) Reducing the cycle time from preparation to go live.