In order to improve the efficiency of agricultural product logistics transportation, based on big data technology, this paper starts from the factors that affect the efficiency of agricultural product logistics and combines big data technology to conduct the research on the mechanism and efficiency of agricultural products logistics transportation. Moreover, this paper analyzes how to improve the efficiency of agricultural product logistics by studying the dynamic relationship between influencing factors and the efficiency of agricultural product logistics. At the same time, this paper takes the efficiency evaluation of agricultural product logistics transportation network as the research object to improve the agricultural product data analysis algorithm, and constructs the system model from the perspective of the supply chain. In addition, this paper constructs system function modules according to the actual needs of agricultural product logistics transportation, and analyzes agricultural product transportation logistics by factor analysis. Finally, this paper verifies the effect of the model proposed in this paper through experimental research. From the test results, it can be seen that the model proposed in this paper basically meets the actual needs.