Compared to conventional heat conduction heating, microwave heating has the effect of internal and external heating and has been widely used in various fields such as industry and agriculture. Nevertheless, the problems of low heating efficiency and low heating uniformity in industrial applications are still widespread. A heating method based on dual-port non-synchronous rotating structure is proposed to reduce the mutual coupling between ports, and a microwave heating model of dual-port rotating structure is established based on COMSOL multiphysics. This paper analyzes the effect of the rotation speed between the two microwave source ports on the mutual coupling and heating uniformity between the ports, realizes the low mutual coupling and high uniformity heating between the ports, and greatly improves the efficiency of microwave heating.