Subassembly has an important role in aircraft manufacturing. There are different shop orders at different periods, so subassembly system need to adjust production capacity through reallocation of resources. Based on graphic ant colony algorithm(GACA), an optimal resource allocation method was proposed on aircraft subassembly system. In the method, first, a Petri Net(PN) model was used to describe the logic of tasks and resources in system. Next, to support solving process of GACA, structure graph for ant routing was designed by PN model. Then according to features of aircraft subassembly, solving rules and procedures of GACA are discussed in detail, which can obtain an optimal resource allocation scheme by requirement of production capacity adjustment. In addition, an example on flaperon assembly was introduced and the result demonstrated the functionality of the method.