This paper introduces export tax rebate and iceberg transportation cost in new economic geography into the analysis framework of heterogeneous enterprise trade model and discusses the influence of export tax rebate policy on the export intensity of enterprises from the perspective of domestic transportation infrastructure construction. It is found that the increase of the export tax rebate rate significantly improves the export intensity of enterprises on average. The level of domestic transportation infrastructure generates an adjustment effect on this promotion effect, and the adjustment direction mainly depends on the relative size of the transportation distance between enterprises’export domestic section and domestic trade transportation distance. The results show that the cooperative implementation of export tax rebate and transportation infrastructure policy is beneficial to improving the export intensity of domestic enterprises, especially those in the central and western regions, enhancing the vitality of regional development and promoting regional coordinated development. On the one hand, a new explanation to understand the regional heterogeneity effect of export tax rebate is provided via the perspective of domestic transportation infrastructure construction; on the other hand, corresponding policy suggestions on how to promote the implementation of regional coordinated development strategy are provided under the new development pattern.