With China’s entry to World Trade Organization in 2005, the period of protection for agricultural products was over. Chinese agricultural products compete directly and intensely with international counterparts. On this condition, this paper uses DEA advantage efficiency model and disadvantage efficiency model to make an assessment of agricultural production efficiency with samples of 31 provinces of China. By Calculation, we have got a list of ranks with agricultural comprehensive efficiency. Through inter-simple sequence repeat (ISSR) analysis, the agricultural production efficiency is classified and ranked. The results have a great of referenced values for getting to know correctly China agricultural production condition and making related agricultural policy.