This study used nickel wire to trap the magnetotactic bacteria which had adsorbed Au(III), and a magnetic separation model was built to describe this process. Kinetics of the movement of metal loaded bacteria in the whole magnetic field was investigated both experimentally and theoretically. It was found that the magnetic intensity had evident effect on the separation efficiency, but little effect on the separation rate. The period of trapping bacteria to capacity for the nickel wire was proved about 100 minutes. It was found that the trapped bacteria were deposited in multi-layers, showing the ability of multi-layer trapping for the wires. The theoretical results could reach a good agreement with the experimental, which indicated the feasibility of applying the model to the optimization of magnetic separation process using magnetotactic bacterium.