This paper presents MIMO fuzzy logic system for control of the parameters of an autonomous system for cooling of the cutting tool on three axis milling machine with CNC, which controls voltage of the FET gate, thereby changing the temperature of the Peltier element, and the voltage on the fan used to cool the warm side of the Peltier element. Accordingly, the fuzzy logic control system has two input and two output variables. The input ones are the temperature in the cutting zone and the temperature of the warm side of the Peltier element, and the output voltage at the gate of a field effect transistor and the voltage at the fan. Simulation of the fuzzy logic system was carried out by numerical methods using soft and hard arithmetic operations, as well as different operators of fuzzy implications for hard arithmetic operations. In modeling of the fuzzy logic of MIMO system for control of the parameters of an autonomous system for cooling of the cutting tool in the task of operation of CNC equipment, different operators of the fuzzy implications were obtained and graphs were compared of the voltage on the fan and of the temperature on the warm side of the Peltier element. Their strong and weak points were identified. The best results were obtained employing the soft arithmetic operations, the use of which for the fuzzy logic of MIMO system generates the necessary voltage value for the gate of the MOSFET and the fan depending on the temperature in the cutting zone and on the warm side of the Peltier element.