This study develops a nanocomposite structure with magnetism and biocompatibility. Composite structures with magnetism can be applied for biomarkers, specific tissue cell detection and targeted drug therapy. This study adopts a chemical disposition method to prepare Fe3O4 magnetic nanoparticles with the average size of 20-25nm. The complex biocompatible chitosan-alginate membrane covers Fe3O4 magnetic nanoparticles and the thickness of the complex membrane is controlled at 50-80nm. The efficiency of the oligonucleotide (ODN) combination is increased through the high biocompatibility of this composite film. Two groups of different sequences of ODNs and a bridge ODN undergo hybridization. The results show that the intensity at which the Fe3O4 is covered by chitosan-alginate composite film conjugated with ODNs is 2300nN. Furthermore, Fe3O4 covered by complex membrane of chitosan-alginate hybridized with 30 μM ODNs to yield the optimum hybridization intensity of 4528 nN, and the average hybridization intensity of ODNs with different concentration is 3971 nN.