Cognitive Wireless Mesh Networks (CWMN) is a novel wireless network which combines the advantage of Cognitive Radio (CR) and wireless mesh networks. CWMN can realize seamless integration of heterogeneous wireless networks and achieve better radio resource utilization. However, it is particularly vulnerable due to its features of open medium, dynamic spectrum, dynamic topology,and multi-top routing, etc.. Being a dynamic positive security strategy, intrusion detection can provide powerful safeguard to CWMN. In this paper, we introduce trust mechanism into CWMN with intrusion detection and present a trust establishment model based on intrusion detection. Node trust degree and the trust degree of data transmission channels between nodes are defined and an algorithm of calculating trust degree is given based on distributed detection of attack to networks. A channel assignment and routing scheme is proposed, in which selects the trusted nodes and allocates data channel with high trust degree for the transmission between neighbor nodes to establish a trusted route. Simulation results indicate that the scheme can vary channel allocation and routing dynamically according to network security state so as to avoid suspect nodes and unsafe channels, and improve the packet safe delivery fraction effectively.