Due to the explosive growth of data demand from mobile devices, cellular operators have been exploring the use of WiFi to offload traffic from the LTE network. Such an integration opens the door for exploiting the network usage diversity for further overall network performance improvement, by intelligently and dynamically scheduling flows over the most appropriate network. However, how such a function can be efficiently and systematically realize, is missing from the current standard specifications, especially on the network infrastructure side. In this paper, we aim to solve such a challenge by proposing a Software-Defined Networking (SDN) based flow scheduling system that is compatible to the 3GPP LTE-WiFi integration framework. The global view provided by SDN makes it easy to collect necessary flow information, and the flexible control of SDN enables efficient flow scheduling. We view the flow scheduling problem as an overall network utility maximization problem. We prove its hardness and propose an approximation algorithm for solving the problem. The proposed system can be incrementally deployed over existing wireless network infrastructure. With extensive simulations in NS3 and demo implementation, we prove the feasibility and effectiveness of both the framework and the scheduling algorithm.