Taking ecological benefits outputs into composition of index system, the efficiency of infrastructure investment is evaluated by SBM-Undesirable model, and spatial differences are processed by ArcGIS and Geoda model, based on data from 31 provinces in China. The conclusions are conducted as follows. Firstly, infrastructure investment efficiency in China is generally at a low level, and there are large differences among regions, in which the eastern shows the highest infrastructure investment efficiency, followed by the central region, and then the western region. Secondly, a significant positive spatial autocorrelation of infrastructure investment efficiency shows in each region, after the analysis taking the global Moran's I index. Thirdly, high spatial stability for infrastructure investment efficiency in most regions in China, taking the methodology of the LISA agglomeration plot and significance level plot. Then the suggestions are proposed including expanding input of infrastructure investment, highlighting cooperation among regions and promoting technology innovation in enterprises, to increase the efficiency of infrastructure investment.