The advanced fighter should possess the performance such as super-sound cruising, stealth, agility, STOVL(Short Take-Off Vertical Landing),powerful communication and information processing. For this purpose, it is not enough only to improve the aerodynamic and propulsion system. More importantly, it is necessary to enhance the control system. A complete flight control system provides not only autopilot, auto-throttle and control augmentation, but also the given mission management. F-22 and JSF possess considerably outstanding flight control system on the basis of pave pillar and pave pace avionics architecture. But their control architecture is not enough integrated. The main purpose of this paper is to build a novel fighter control system architecture. The control system constructed on this architecture should be enough integrated, inexpensive, fault-tolerant, high safe, reliable and effective. And it will take charge of both the flight control and mission management. Starting from this purpose, this paper finishes the work as follows: First, based on the human nervous control, a three-leveled hierarchical control architecture is proposed. At the top of the architecture, decision level is in charge of decision-making works. In the middle, organization & coordination level will schedule resources, monitor the states of the fighter and switch the control modes etc. And the bottom is execution level which holds the concrete drive and measurement; then, according to their function and resources all the tasks involving flight control and mission management are sorted to individual level; at last, in order to validate the three-leveled architecture, a physical configuration is also showed. The configuration is distributed and applies some new advancement in information technology industry such line replaced module and cluster technology.