An apparatus and a method for indirectly cooling a superconducting quantum interference device (SQUID) are provided. The apparatus includes an outer container extending in a vertical direction; a metallic inner container inserted into the outer container to store a liquid coolant, the metal inner container including a top plate; a SQUID sensor module disposed between a bottom surface of the outer container and a bottom surface of the inner container; a heat transfer pillar adapted to cool the SQUID sensor module, the heat transfer pillar having one end connected to the bottom surface of the inner container and the other end directly or indirectly connected to the SQUID sensor module; a magnetic shield part formed of a superconductor covering a top surface of the SQUID sensor module; and a heat conduction plate being in thermal contact with the other end of the heat transfer pillar.