This article presents the results of the simulation of an automatic control system for the heat supply of a greenhouse complex with a geothermal heat source, conducted in order to study the possibility of geothermal heat supply system automation. Scilab version 6.1 was used for simulation. Based on the results of the simulation, the optimal mode of the automation system function of the heat exchanger primary circuit was developed and implemented. Reagentless treatment of geothermal water in the heat supply system with an acoustic–magnetic device (designed and patented by the authors of this paper) can significantly reduce the intensity of scale formation in the heat exchanger and geothermal heat supply system equipment. It provides conditions for the automation of geothermal heat supply systems of greenhouses with a surface heat exchanger. Using an automation system allows greater accuracy and reliability in maintaining the required temperature regime (18–20 °C) in the greenhouse, reduces the frequency of system shutdown for unplanned cleaning of the heat exchanger and equipment, reduces the complexity of manual operations of heat exchanger and equipment maintenance (removal of sludge, scale) and reduces the economic costs of transportation and heat consumption.