Abstract:Efficient and adequate production and supply of green agricultural products is an important part of the establishment of food safety system in China ,in the meantime,it can satisfy consumer pursuit of quality of life and health needs. Based on the relevant literature, this article constructs a new evaluation index system by emphasis on four aspects:the economy, supply chain operations,innovation and the environment.This paper evaluates supply chain of green agriculture performance by taking 10 cities of Shandong Province for examples,thought using dimensionality reduction capabilities of Principal component analysis combined with the BCC model of DEA . Contrast the data find the problems and puts forward to enhance the effectiveness performance of supply chain.The research indicates that ,Heze, dongying, zibo, linyi city,the performance levels of the green agriculture supply chain are below the average effective. There are many problems such as mismatch between input and output of production factors, lack of science and technology innovation,low utilization rate of resources and effect of brand.