Magnetic nanoparticles have been widely applied to biomagnetism, such as drug deliver, magnetic labeling, and contrast agent for in vivo image, etc. To localize the distribution of these magnetic particles in living organism is the first important issue to confirm the effects of magnetic nanoparticles and also evaluate the possible untoward effects. In this study, a scanning high Tc rf-SQUID superconducting quantum interference devices (SQUIDs) biosusceptometry, composed of static SQUID unit and scanning coil sets, is developed for biomedicine study with the advantages of easy operation and unshielded environment. The characteristics tests showed that the system had the low noise of 8 pT/Hz at 400 Hz and the high sensitivity with the minimum detectable magnetization around 4.5 × 10-3 EMU at distance of 13 mm. A magnetic nanoparticle detection test, performed by ex vivo scanning of the magnetic fluids filled capillary under swine skin for simulation of blood vessels in living bodies, confirmed that the system is feasible for dynamic tracking of magnetic nanoparticles. Based on this result, we performed further studies in rats to clarify the dynamic distribution of magnetic nanoparticle in living organism for the pharmacokinetics analysis like drug delivers, and propose the possible physiological metabolism of intravenous magnetic nanoparticles.