Yolk/shell particles, which were hollow silica particles containing a movable magnetic silica core (MSC), were prepared by removing a middle polystyrene layer from multilayered particles of MSC/polystyrene/silica shell with heat treatment followed by a slight etching with a basic solution. An ac electric field was applied to the suspension of the yolk/shell particles to form pearl chains (1D structure) of yolk/shell particles. Observation with an optical microscope showed that the MSCs in the silica compartment of the pearl chains had a zigzag structure under the electric field. An external magnetic field applied to the suspension could form a novel structure of doublet MSC in the shell compartment of the quasi-pearl chain structure. Application of a magnetic field was also performed for 2D hexagonally close-packed assemblies of the yolk/shell particles, which could two-dimensionally form a doublet structure of MSCs as if they were polarized in the compartment. Switching on/off the magnetic field successfully controlled the positional ordering of cores in the consolidated silica shell.