Aiming at the mutual coupling of multiple physical fields in the microwave heating process and the generation of thermal runaway phenomenon, in this paper, a cooperative variable power heating strategy with multi-microwave source clusters under dynamic switching topology is proposed in order to improve the temperature uniformity. Firstly, an algebraic graph theory is used to establish a communication topology for complete information transfer, which is used to construct a distributed structure among multiple microwave source intelligences. Secondly, the dynamic topology switching algorithm under event triggering is introduced, and the real-time temperature distribution of the heated materials is considered to achieve the dynamic switching of the topology connection mode between microwave source clusters in order to synchronously coordinate the power consistency output between different clusters. On this basis, a numerical calculation model is constructed to solve the mixed optimization of integer and continuum variables by means of the finite element method. Finally, the effectiveness of the heating strategy to improve temperature uniformity is verified by microwave heating SiC media simulation calculation. The numerical calculation results show that the temperature uniformity indexes are improved by 34.1%–50.4% and 28.1%–55.2% in each horizontal and vertical section for single materials, and by 59.1%–59.7% and 46.5%–63.4% in each horizontal and vertical section for multi-materials, respectively, in comparison with the general heating method. This strategy effectively avoids the residence of hot and cold spots in the material, which in turn optimizes the temperature distribution.