Immunomagnetic beads separation (IMBS) technique plays more and more important roles in biological detection recently. One of the key technologies for immunomagnetic beads separation is the magnetic nanobead separator (MNS) which is capable of providing a magnetic field of high intensity and high gradient. The innovative MNS was constructed by NdFeB magnetic tile blocks and permalloy clinohedral magnetizers. There are six separation holes on this annular MNS providing with the magnetic field of high intensity and high gradient. The MNS was successfully applied in the field of nanobead magnetic separation on both Escherichia coli and avian influenza virus. The magnetic intensity measurement results show that the highest MNS magnetic field intensity of 1.44T and the highest MNS magnetic field gradient of 96.3T/m (865.5cm3 volume, 4.8kg weight) were achieved. The measurement average relative error among each hole of the four sets of MNS was between 2.0% to 3.3%. The study results also show that MNS volume, material and profile of magnetizer have different effects on the intensity and gradient of magnetic field. The larger MNS or the MNS with permalloy magnetizer or with sidleingmagnetizer can obtained higher intensity and gradient of the magnetic field compared to the smaller MNS or MNS with soft iron magnetizer or MNS with straightshape magnetizer. Therefore, according to different IMBS application requirements, it can be obtained the ideal separator easily with different structure elements.