In this paper, we developed a multi-protocol controller based on SoC and embedded Linux and applied it to integrate with BAS in a unified TCP/IP socket communication. The multi-protocol controller integrates control networks of RS-485 and LonWorks devices to BAS. The system consists of three-tier architecture, such as a BAS, a multi-protocol converter, and control devices. By using UML, we modeled the system architecture. In order to show the feasibility of system architecture, it was applied to a small BAS system. The experimental results show that the multi-protocol controller using embedded Linux is flexible and effective way to develop a building control system.