Abstract: software-defined networking (SDN) separates the control plane and the data plane, and this kind of separation can achieve flexible control via deploying fine-grained rules on the flow tables in switches, while potentially improving the utilization of network bandwidth. With the development of SDN, more and more campus and enterprise network begin to deploy network based on SDN. During this procedure, SDN has encountered some problems which dont exist in the traditional IP network. For example, some protocols used in the existing IP network are subject to great challenge in SDN based network, such as TCP, which is the most basic protocol in TCP/IP network. First, we make a penetrating analysis on the working mechanism of SDN, and three examples are given to illustrate that it is quite possible to generate large volume of Packet-In messages even in proactive mode. Then experiments are carried out and the results show that the end-to-end TCP connections have experienced a large delay caused by the SDN unique operations such as re-organizing of rules in TCAM and fast Packet-In message generating. In the worst case, the delay caused by the reordering of the rules can reach up to 10 seconds when the TCAM contains 4000 flow entries in our experiments. Based on the experimental results, we highlight two major problems when applying traditional TCP protocol in SDN networks: one is that it is hard to establish the connection, and the other is the transmission inefficiency. Through the analysis of the experimental results, we propose the possible direction to solve TCP inefficiency issue in SDN.