Perimeter control based on Macroscopic Fundamental Diagram (MFD) aims to meter the number of transferring vehicles at the periphery of the protected urban region in order to obtain the desired number of vehicles in that region. The advantage of perimeter control is less computational effort, while its drawback is that it may create long queues and delays at the perimeter of the controlled area. For capturing boundary queue dynamics, an enhanced accumulation-based MFD model is proposed using colored Petri Nets by considering transfer flows, boundary queues and travel delays simultaneously. The gated intersections and related road segments on the border of a protected region are modeled as so-called boundary buffers. Based on the enhanced MFD model, anintegrated perimeter control framework is proposed with consideration of travel time and queuing time in buffers. In this framework, the controllers between peripheral and protected region are optimized using model predictive control theory. Then, internal flow controllers are adopted to homogenize traffic density among subregions, and route guidance is also used to balance the number of queuing vehicles among boundary buffers. Simulation results verify the effectiveness of the proposed integrated perimeter control. Furthermore, the impacts of buffer storage capacity on region heterogeneity and trip completion rates are also investigated in this paper.