This paper points out the main issue of our building automation system is that the system has been integrated as weak current, which leads to be incompatibility between automation system and facility. It analyses the integration objectives, phrasing and evaluation criterion of facility automation system, and proposes the integration method about automation system and facility system in protective engineering, which aimed at the function of system, enhanced the coordination between automation system and facility system in all aspects of design, construction, programming and debugging, and even the development stage of product and management strategies.