In the heating and drying system using microwaves, an optimal design method was presented to effectively shield microwaves leakage between the door and the cylindrical applicator. In order to protect the human body from leaking microwaves, it is necessary to keep the intensity of microwaves below 5 mW/cm². The door part adopts a choke structure and includes a number of design factors, such as, fin shape, slit shape, and a gap between the applicator and the door. The geometry was optimized by design of experiments, applying full factorial design and response surface method in a 4-factor, 2-level design. The results obtained by ANSYS HFSS analysis were applied to the intensity of microwave leakage according to the change of the design factors. The shape of the choke structure was optimized using Minitab, a statistical program. The microwave heating and drying system was manufactured based on optimal design value and the leakage of microwaves between the door and the applicator was measured. We confirmed that the experimental values were consistent with the simulation values.