In order to analyze the moisture distribution of rough rice with high moisture content within counter flow drying layer and achieve the dynamic tracking of drying process and its control, based on the moisture diffusion model of drying process and the mass conservation equation of deep bed drying process, grain moisture variation in counter flow drying process was analyzed, and the moisture distribution in grain layer and the analytic expression of drying rate were deduced. Experiments indicate that 50℃ hot air still has drying capacity after penetrating a 0.5m thick refluxed zone when the ratio of air flux to grain mass is 4. The deviation of grain moisture from discharge hopper between mathematical explanations and experimental results was within ±0.5%, and it confirmed the reliability of the analytical model.