Adaptive optimization is one of the means that agile organization of command and control resource (AOC2R) adapts for the dynamic battlefield environment. A math model of the adaptive optimization of AOC2R is put forward by analyzing the interrelating concept and research. The model takes the adaptive process as a multi-stage decision making problem. The 2-phases method is presented to calculate the model, which obtains the related parameters by running the colored Petri net (CPN) model of AOC2R and then searches for the result by ant colony optimization (ACO) algorithm integrated with genetic optimization techniques. The simulation results demonstrate that the proposed algorithm greatly improves the performance of AOC2R.