The invention discloses a calibration method for a multichannel SQUID (Superconducting Quantum Interference Device) biological magnetic system, which is a calibration method in which room temperature and low temperature are united. The equivalent error area of a gradiometer is determined by room temperature calibration, and the voltage coefficient of a system magnetic field is calibrated by usingthe uniform magnetic field generated by a Helmholtz coil, corresponding voltage signal output by the system and measured error area at low temperature. The invention comprises the following steps of:(1) calibrating room temperature for equivalent error area of the gradiometer; (2) installing an SQUID biological magnetic system; and (3) calibrating low temperature by the Helmholtz coil. The invention is characterized by calibrating the system by means of the consistency of the room temperature and low temperature equivalent error areas and has the advantages of avoidance of spatial positioning precision and calculation caused by the single low temperature coil, simple operation, simultaneous calibration of multichannel and good consistency.