This paper proposes a macroscopic fundamental diagram (MFD)-based perimeter control approach for coordinated ramp metering, aiming to minimize the total time spent (TTS) of a freeway network (stretch) with multiple bottlenecks. To address problems incurred from limited queue storage space and minimum green time at on-ramps, the proposed method extends previous approaches in two aspects. Firstly, a coordinated ramp control approach is proposed to ensure that the total metered on-ramp flow remains below the value determined by the MFD-based perimeter regulator, thereby preventing network over-saturation. Secondly, a novel queue management approach is developed to prevent on-ramp queue saturation and its associated side effects, for example, spillback or insufficient control actions. This approach determines the quasi-optimal flow of the next upstream (slave) on-ramp, based on the predicted queue of each (master) on-ramp suffering from excessive queues. The proposed perimeter controller was tested using SUMO, a microscopic simulator, on a realistic freeway network, and compared with other existing strategies, including HERO and perimeter controllers with other metered on-ramp flow distribution approaches. The simulation results suggest that the proposed strategy can ( i) effectively mitigate congestion and maintain capacity within the freeway network, resulting in reduced overall TTS, and ( ii) appropriately delay or prevent queue saturation at on-ramps.