The technological process of agricultural production is inextricably linked to the movement of a large number of goods, ranging from the supply of raw materials to their conversion and delivery of finished products. In the implementation of freight flows at the enterprises of agro-industrial complexes and the complex mechanization of raw material conversion processes, the main role is played by systems of transport and technological machines, which include screw conveyors with the ability to convert materials. For this purpose, the simultaneous performance of transportation and separation processes has been studied. The results of the investigation include the construction and study of the mathematical model of the system «a screw of the screw conveyor—grain mixture and separation process» involving further experimental research. The study of the effectiveness of separating agricultural materials with a multifunctional screw conveyor-separator showed that for effective sifting, the selected rational values of the parameters lie within the following limits: angle of inclination of the sieve was 0–14°, and frequency of rotation of the working body was 300–700 rpm. Some rational parameters were obtained during the grain mixture separation process on the basis of an experimental study, namely: n = 380 rpm; q = 0.9–4.7 kg/h·cm2, γ = 0–14°; P = 0.22–0.7 kW, depending on the size of the working sieve (100 × 200 mm). These rational parameters will make it possible to increase the efficiency of agricultural materials separation by a screw conveyor separator, to achieve maximum productivity, and to reduce energy consumption compared to other sorting devices.