This paper presents a methodology for multi agent negotiation in value-based decision on building system selection. It consists of methods and knowledge acquisition, negotiation protocols, and model of the agent negotiation. The project management of research including review of research positioning in domain of computer application in value engineering, data necessary and analysis, agent methodology. Results presented are knowledge of building system (roof system) with a model of decision-making using Analytical Hierarchy Process (AHP) based on three-stakeholder preferences and concept of protocol negotiation. This methodology combines value analysis method, decision method and multi agent development method. FAST analysis is a tool for value analysis. AHP is a tool for decision process. Prometheus model has been used for developing a negotiation agent. © 2008 IEEE.