With a great variety of crop categories, Jilin Province is the main grain producing area in China, but agricultural product logistics is developing slowly. Based on the input-output data of agricultural product logistics in Jilin Province from 2009 to 2018, this paper conduct an empirical study on the efficiency of agricultural product logistics in Jilin Province with Deap2.1 software by means of CCR and BCC models in data envelopment analysis. The research results show that there are still some deficiencies in the investment of fixed assets and professionals etc. in agricultural product logistics in Jilin Province, and the scale effect has not yet been realized, and the overall capacity of agricultural product logistics is weak; This paper puts forward the reasonable allocation of input resources from the three levels of government, industry and logistics subjects, to improve the management level of agricultural product logistics and realize the cost reduction and efficiency increase.