Abstract: The input-output index system of urban agglomeration highway traffic efficiency was provided from the perspective of urban agglomeration highway transportation system based on the input-output aspects, the data envelopment analysis (DEA) model and the A-prefer-DEA (PDEA) model were then established in this paper. Furthermore, the highway traffic efficiency of the three urban agglomerations called Chang-Zhu-Tan, Yangtze River Delta and Pearl River Delta was effectively calculated and comprehensively evaluated. Traditional DEA model shows that the highway traffic efficiency of ChangZhu-Tan urban agglomeration is DEA weak efficiency, however, the highway traffic efficiency of Yangtze River Delta and Pearl River Delta are DEA efficient. The evaluation results based on PDEA model are more intuitive, the highway traffic efficiency value of Yangtze River Delta, Pearl River Delta and ChangZhu-Tan is 1.678 2, 1.577 9 and 0.866 2, respectively. Therefore, the gap between Chang-Zhu-Tan highway traffic efficiency and those of Yangtze River Delta, Pearl River Delta is apparent based on PDEA model.