Abstract: The article uses the Malmquist index method, Investigating the fluctuant trend of Shandong Province agricultural total factor productivity from 2000 to 2011 year, through the Malmquist index decomposition, analyzing the intrinsic motivation of Shandong Province agricultural total factor productivity. The results showed that the agricultural total factor productivity grew at 0.5% annually from 2000 to 2011, wherein, agricultural technical efficiency grew at 1% annually, the agricultural technology progress index fell 0.5% annually, technical progress decline hindered agricultural total factor productivity growth; from the cities situation, there are 10 cities in total factor productivity growth, there are 7 in total factor productivity drops, most technical efficiency to do more effective, technological progress needs to be improved.