The invention provides a packaging structure of a superconducting quantum interference device. The packaging structure comprises the components of a packaging trough of which the bottom and the side walls are provided with a lowpass filtering layer; a bottom board which is fixed on the surface of the lowpass filtering layer at the bottom of the packaging trough and is provided with a device leading-out electrode; the superconducting quantum interference device which is fixed on the bottom board and realizes electric connection; and a cover board which hermetically covers the packaging trough for forming an accommodating space, thereby packaging the superconducting quantum interference device in the accommodating space, and furthermore one surface, which faces the packaging trough, of the cover plate is provided with a lowpass filtering layer, wherein the lowpass filtering layer comprises a mixture layer which is composed of metal powder and a low-temperature glue. According to the packaging structure, a shielding layer which is composed of metal nanometer particles is added into the packaging structure of the superconducting quantum interference device, thereby effectively preventing entry of an external RF electromagnetic field into the superconducting quantum interference device. Furthermore the insulating characteristic of the low-temperature glue realizes a fact that the shielding layer cannot form a conducting loop, thereby preventing generation of a metal eddy current and improving stability of the superconducting quantum interference device.