Magnetic nanomaterials have drawn ample attention in the field of biotechnology due to their excellent magnetic properties and biocompatibility. These materials have been widely used for exosome isolation, DNA separation, magnetic resonance imaging, and drug delivery. However, their application in cell isolation has been limited due to the lack of efficient antibody conjugation and instability in aqueous solutions. In this study, we produced hybrid maghemite nanorod/immuno-microgels with high capturing capacity for cell isolation and enumeration. Lepidocrocite (γ-FeOOH) and maghemite (γ-Fe2O3) nanorods with controlled morphology are synthesized using hydrolysis method. The effects of the different synthesis conditions on morphology, phase composition, and magnetic properties of lepidocrocite are studied to determine the best synthesis conditions. We coat the nanorods with chitosan and attach them to the poly(N-isopropylacrylamide-co-acrylic acid) (PNIPAM-AA) microgel through chemical bonding to form a nano/hybrid microstructure. Our results suggest that the hybrid magnetic microgels have more antibody binding capacity and higher cancer cell capturing rate compared to pristine maghemite nanorods. In addition, new cell magnetometery method was applied for cancer cell quantification after capturing step in which different magnetized labelled cells were correlated to the saturation magnetization. In this method, higher concentrations of the primary cell suspension resulted in more binding of the magnetic immuno-microgels to the cells which was shown as saturation magnetization drop in the microgel-cell complex.