In order to effectively promote the development of transportation and regional economy, it is necessary to comprehensively evaluate the efficiency of regional transportation resource allocation. By constructing the index system of traffic resource allocation efficiency, a Three-stage DEA bootstrap model is proposed to evaluate the regional traffic resource allocation efficiency. The Three-stage DEA model is used to eliminate the environmental errors in the evaluation process, and the bootstrap method is introduced to overcome the internal dependence of the effectiveness value of the DEA model. A case study is conducted in 11 regions of the Yangtze River economic belt. The results show that, excluding the influence of environmental factors and random interference, the allocation efficiency of traffic resources in the Yangtze River economic belt is 0.612, Compared with the first-order DEA, the calculation efficiency is reduced by 0.189. Solving the technical input redundancy and promote the development of scale efficiency are the key to the efficient allocation of traffic resources in the region. It can be seen that this method can effectively avoid the deviation of traditional DEA method in evaluating the efficiency of resource allocation, and effectively evaluate the efficiency of regional traffic resource allocation.