Complex systems consist of a large number of entities with their independent local rules and goals, along with their interactions. In the operations of complex system, such as naval ship, proper decisions and controls are required to keep the system working functionally and effectively. An Integrated Reconfigurable Intelligent System (IRIS) framework is proposed for facilitating the design and operation of such naval complex systems through increased automation and reconfigurability. With the reconfigurable systems, the IRIS designed ship will assess the incoming information and then configure itself into the mode most adequate to deal with the situation under consideration. The study in this paper presents a hierarchical control architecture to deal with ever-evolving real time information and making autonomous control for achieving the reconfigurability of naval ship. The control architecture consists of three levels working together to achieve the overall operational goal. It is implemented on a resource allocation problem for a chilled water system. The successful resource allocation leads to a reconfiguration of the system which is the most suitable to handle the situation at hand.