Transportation as a means to support industrial development can impact the economic development of important agricultural heritage sites. Because the central towns in mountainous areas have weak economic interactions with each other, an appropriate method is needed to evaluate their transportation accessibility. This paper takes the Honghe Hani Rice Terraced System (HHRTS) as a study area and develops a model to determine shortest time-distances from central towns in the study area to the nearest high-grade city as a way to evaluate transportation accessibility (TA). We then analyze the relationship between the accessibility of these towns and their economies. The study finds that the TA of the central towns in HHRTS is not good as a whole. More than 70% of the towns are more than 1 hour away from their nearest high-grade city. Of the four counties in the study area, Yuanyang County has the best traffic conditions, while Lvchun County has the worst traffic conditions. The central towns in the northern and middle regions have better TA than those in the west, southwest and east margin regions. The small-scale rural economy has little dependence on the transportation network, while secondary industries are obviously impacted by the transportation network. In the future, to support the integrated development of industries in HHRTS, traffic conditions in each town should be improved appropriately according to the industrial orientation of the town, but excessive investments to construct roads irrespective of eco-environmental impacts and economic benefits should be avoided. Especially in the case of ecologically vulnerable towns, the building high-grade roads should be banned.