This study is focused on surface-modified Fe3O4@SiO2 particles with precisely controlled sizes and shapes applied in magnetorheological (MR) fluids. After the preparation of the monodisperse spindle-shaped and cubic Fe3O4@SiO2 particles, surface modification with dodecyltrimethoxysilane (DTM) was carried out via a silane coupling reaction to increase the dispersion stability of the particles. Afterward, MR fluids were prepared by mixing the DTM-modified Fe3O4@SiO2 particles with silicon oil. Transmission electron microscopy observations demonstrated that spindle-shaped Fe3O4@SiO2 particles could form a more stable chain-like structure than cubic Fe3O4@SiO2 particles upon application of an external magnetic field. The rheological measurements of MR fluids also indicated that the surface modification with DTM, the introduction of anisotropic shapes, and the increase in the particle size all played positive roles in the improvement in MR properties.