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This paper presents the problem of performance degradation due to congestion in multi-channel WMNs. Following the analysis of available solutions to this problem, a cross-layer congestion control scheme MCAP (multi-channel adaptive pacing) is presented, able to obtain higher channel utilization and meanwhile improve the fairness between flows. In MCAP, flows are restricted to inject packets into the WMN at ingress routers according to the available bandwidth estimated for each flow. Furthermore, when a router suffers from high contentions, the packets to be sent from it are coordinated and transmitted in group, which is to improve multi-channel utilization and relieve congestion. Extensive simulations show that MCAP achieves significant improvement in both the network throughput and the fairness between flows, and it also greatly reduces the average network.