In this article, we examine the Total Factor Productivity (TFP) of agricultural and sideline food processing industries from the angle of microscopic, by constructing a Distance Function and Malmquist TFP index model. Our empirical work uses the unbalanced panel data of 545 sample companies of agricultural and sideline food processing industry in China, during the period of 2004 to 2007. The final results show that the TFP indices have a fluctuation within a narrow range, which mainly come from technical change rather than efficiency change during the report period. On the other hand, we find that the vast majority of agricultural and sideline food processing companies in our country are in the state of small scale and technical inefficiency.