The paper presents a mathematical model that characterizes the process of threshing and separation from the threshing machine with an axial flow of a thresher, taking into account the following input parameters: material flow, rotor speed, distance between rotor and counter rotor, mean density of processed material, feed speed, length of thresher and separating surface. Output parameters, such as the distribution function of separated seeds, distribution density function of separated seeds and distribution function of free seeds in the threshing space, as well as the distribution function of unthreshed seeds, together with the value of evacuation losses, were used to control the modeling process.