Macroscopic fundamental diagram (MFD) characterizes a unimodal and low-scatter relationship between traffic accumulation and trip completion rate for homogenous urban network, providing a new perspective for the development of regional congestion control strategies. This paper contributes to the state-of-the-art by proposing a perimeter traffic control strategy for single urban congested region with MFD model and boundary conditions. For an urban protected region, the MFD is introduced to capture network traffic dynamics and optimal capacity. When regional accumulation exceeds the optimal capacity, the restricted inflow distribution considering boundary condition constraints of real-time traffic flows and queue dynamics is used to formulate a perimeter traffic flow control strategy for adjusting traffic signal timing on the periphery of region. To proactively reduce the possibility of queue spillbacks at border links, the dynamic queue-dependent border gated points are also integrated into the proposed control method. The simulation experiment was performed using part of urban network in Jinan, China. The results demonstrate the proposed perimeter control method alleviates the issue of congestion and improves traffic performance in the protected region and at the boundaries.