Aiming at solving the problem in grain drying, with many uncertain influence factors, that the measurement results hysteresis exists, the selection approach was presented on both the controlled and control variables of the continuous flow grain drying. Based on experimental data, factors affecting grain drying process and multiple factors sensitivity affecting grain outlet moisture content were analyzed. The result shows the major factors influencing the grain outlet moisture content sensitivity are discharge motor rotation speed, heated air temperature and initial moisture content; ambient temperature and initial temperature etc. also have effects on grain outlet moisture content sensitivity to a small extent. A control structure of the automatic control system for continuous flow grain drying was designed, and a restraint approach for the measurement lag was introducing differential block.