Transportation infrastructure has spatial spillover effect on economic development via boosting factors flowing between different places. By using China’s 30 provinces （municipalities and autonomous regions） panel data during 2005-2015 and dynamic spatial Durbin model under different spatial weights, this paper analyzes spatial spillover effect of transportation infrastructure on green total factor productivity （TFP）. The results of empirical study indicate that China’s green TFP growth rate is more slowly than GDP growth, that the spatial spillover effect of transportation infrastructure on green TFP is obviously higher than direct effect, that the positive spillover effect of highway density and railway density is significant and their short-term effect is especially obvious, however, the influence of high-grade roads density on green TFP has “central collapse” phenomenon. Transportation infrastructure construction should be coordinated between different regions so as to bring its promotion of factor flowing into fully play, meanwhile, resource-wasting and environmental pollution should be reduced to the greatest extent in material production, construction and maintaining of transportation infrastructure in order to boost green economic development.