Nowadays, an important aspect for achieving a high level of seed production is the expansion of the range of high-quality seed material, which disrupts the technological process of separation and increases its costs. The purpose of the study is to analyse indented separator cylinders for cleaning small-seed crops and develop an appropriate mechatronic system for their control, the use of which would allow performing the technological process of separation with lower specific operating costs and higher productivity. The presented analysis of the technical support of the process of separation of seed material of small-seeded crops indicates the need to improve indented separator cylinders based on automated control of their parameters using photo or video recording of the seed separation with subsequent processing. It has been established that the determination of formal performance indicators of an indented separator cylinder is not trivial. Based on the results of the analysis, a design and technological scheme of the mechatronic system of an indented separator cylinder has been developed. The difference between the proposed system and the conventional one is that the camera captures the trajectory of seeds. This information is processed in the control unit, which in turn changes the speed of rotation of the gear motor and, as a result, the drum with cells, the angle of inclination of the tray, the angle of rotation of the flap with the stepper motor of the hopper dispenser. These manipulations with the operating parameters of the indented separator allow adjusting it to changes in the seed mixture composition, thereby improving the quality and productivity of separation. In addition, due to the automatic adjustment of the operating parameters of the indented separator, the participation of the operator in the separation process is practically not required, which reduces labour costs