In transportation networks, a spontaneous jamming transition is often observed, e.g. in urban road networks and airport networks. Because of this instability, flow distribution is significantly imbalanced on a macroscopic level. To mitigate the congestion, we consider a simple control method, in which congested nodes are closed temporarily, and investigate how it influences the overall system. Depending on the timing of the node closure and opening, and congestion level of a network, the system displays three different phases: free-flow phase, controlled phase, and deadlock phase. We show that when the system is in the controlled phase, the average flow is significantly improved, whereas when in the deadlock phase, the flow drops to zero. We study how the control method increases the network flow and obtain their transition boundary analytically.