This article considers the implementation of mathematical models and algorithms in the problems of controlling the process of chlorella cultivation. When building a control system, the following tasks are solved: collecting and primary processing of information, predicting the course of technological processes, optimizing regime parameters, managing a technological process, etc. One of the necessary conditions for the optimal conduct of the process of cultivating microorganisms is automatic control of the quality and composition of nutrients at the inlet, as well as control of the output indicators of the process. The frequency of solving control problems is set depending on the technological features, the control object, the mode of introducing the process, and also on the availability of a complex of technical means. As a result of the implementation of the proposed control system, the maximum ratio of the concentration of chlorella from its average value decreased by 23.8%. Thus, the control system for the cultivation of chlorella provides timely forecasting of the course of the technological process and the formation of control actions using a computing device, which contributes to an increase in the productivity of the cultivator by 8-12%.