The fiber-optic radiometric thermometry of surfaces with non-uniform temperature distribution was analyzed theoretically and optimization of fibers positioning was considered. An infrared fiber-optic multi-channel radiometer was used to monitor and control the temperature of samples in a microwave (MW) heating system. Several heater control algorithms were investigated and the optimal control mode was obtained. Preliminary results of biological tissue warming by microwave heating were obtained. This novel control system is reliable and precise. Such a system should be very useful for medical and industrial applications.