A microwave sterilizing device includes a container supplying device, a container transport device, a sterilizing sprayer, a microwave cavity unit and a microwave generating device. The container supplying device may supply containers in a continuous manner. The container transport device has a starting point and an end point and the containers are moved from the starting point to the end point on the container transport device. The container supplying device is disposed near the starting point. The sterilizing sprayer can spray germicide onto the inside and outside of each container. The microwave cavity unit can allow the passage of the containers. The microwave generating device is disposed outside of the microwave cavity unit and can generate microwave which is fed into the microwave cavity unit to heat up the germicide remained on the internal walls of each container so as to sterilize the container.