The invention relates to the technical field of microwave source control, and provides an industrial microwave source layered mixed intelligent control system and control method, which can guarantee the control goal of safe operation of a novel high-power microwave source and realizes high-efficiency application of microwave energy. The control system comprises a sensing layer subsystem for detecting the states of a microwave source and a heated medium, a calculating layer subsystem for setting parameters of the microwave source before heating and performing information processing in the heating process according to the state data of the microwave source and the heat medium acquired by the sensing layer subsystem, an optimization layer subsystem for performing data fusion on the data processed by the calculating layer and configuring an adjustment scheme of the industrial microwave source in real time according to the fused data, and a safety layer subsystem for performing real-time power control over the industrial microwave source according to the adjustment scheme obtained by the optimization layer subsystem.