An efficient multi-objective optimization (MO) algorithm named as NSGA-Ⅱ is applied to solve the problem of organizational design of C2. Before introducing the settings of NSGA-Ⅱ, a discussion is made about the shortcomings in forming optimizing objective by weighted method and proceeding procedure like nested GA, which exist in popular algorithms of organizational design of C2. With this MO algorithm, more indexes can be optimized within one procedure which makes it more practical than dealing with single index as usually. Some modifications are made for NSGA-Ⅱ to match the specifications of the experiment, a group of appealing and inductive results are reached, which reveals the effectiveness of NSGA-Ⅱ in the problem of organizational design of C2.