Based on panel data of 30 provinces，municipalities and autonomous regions from 2000 to 2009 in China,this paper uses stochastic frontier production function to measure the efficiency of agricultural products logistics and discusses exogenous influencing factors affecting the efficiency of agricultural products logistics and the resources of total factor productivity changes.The result shows that the efficiency of China’s agricultural products logistics is inefficient and differences exist in different places.The exogenous influencing factors have positive influence on the efficiency of China，s agricultural products logistics and then Total Factor Productivity Changes is attributed to the combined effects of technological improvement and technical efficiency in China，among which technical efficiency changes are mainly in eastern regions while technical changes are almost entirely in the central and western regions.The improvement of technical efficiency in agricultural product logistics in China is an enormously comprehensive project,which is supported by strategic distribution of regional development from the macroscopic view,and depends mesoscopically on the structural adjustment direction of industrial development,and finally allocates microscopically the flow configuration of staff,materials,capital and information in the logistics core process.