Ranging from computer network to traffic network, complex networks are ubiquitous in our lives. How to control congestion to make network operate more effectively is one of the most essential issues in complex network research. At present, a large number of studies on traffic dynamics mainly focus on single-layer networks. However, in fact, many complex systems are coupled by multiple networks. In this paper, we propose a resource allocation strategy for three-layer network with which the limited total delivery capacity can be reasonably allocated to each node of physical layer based on the degree of nodes in two logical layers. Compared with the average allocation of delivery capacity, the traffic capacity is improved and the network has better transmission performance in average traveling time and average throughput with our strategy.