In recent years, software-defined networking (SDN), which performs centralized network management with software, has attracted much attention. Although packets are transmitted based on flow entries in SDN switches, the number of flow entries that the SDN switches can handle is limited. To overcome this difficulty, this paper proposes a flow-based routing method that performs flexible routing control with a small number of flow entries. The proposed method provides mixed integer programming. It assigns common paths to flows that can be aggregated at intermediate switches, while considering the utilization of network links. Because it is difficult for mixed integer programming to compute large-scale problems, the proposed method also provides a heuristic algorithm for them. Through numerical experiments, this paper shows that the proposed method efficiently reduces both the number of flow entries and the loads of congested links.