In this work, we present the coating regulations of Fe3O4 nanoparticles (NPs) by the reverse microemulsion method to obtain the Fe3O4@SiO2 core/shell NPs. The regulation produces the core/shell NPs with a single core and with different shell thicknesses, and it especially can be applied to different sizes Fe3O4 NPs and avoid the formation of core-free silica particles. Our results reveal that the silica coating parameters suitable for Fe3O4 NPs with certain size are not definitely applicable to that with other sizes, and the match of the number of Fe3O4 NPs with aqueous domain is essential. We found that the small aqueous domain is suitable to coat ultrathin silica shell, while the large aqueous domain is indispensable for coating thicker shells. To avoid the formation of core-free silica particles, the thick silica shell can be achieved by increasing the content of either TEOS through the equivalently fractionated drops or ammonia with a decreased one-off TEOS. The ligand exchange between the intermediate processes of the silica coating is evidenced. Our results provide not only a strategy for synthesizing uniform Fe3O4@SiO2 core/shell NPs with controlled shell thickness, but also a regulation that can be applied to preparation other core–shell NPs.