An effective method was developed for synthesizing magnetite/polymer colloidal composite microspheres with controllable variations in size and shape of the nanostructures and desirable interfacial chemical functionalities, using surfactant-free seeded emulsion polymerization with magnetite (Fe3O4) colloidal nanocrystal clusters (CNCs) as the seed, styrene (St) as the monomer, and potassium persulfate (KPS) as the initiator. The sub-micrometer-sized citrate-acid-stabilized Fe3O4 CNCs were first obtained via ethylene glycol (EG)-mediated solvothermal synthesis, followed by 3-(trimethoxysilyl)propyl methacrylate (MPS) modification to immobilize the active vinyl groups onto the surfaces, and then the hydrophobic St monomers were polymerized at the interfaces to form the polymer shells by seeded emulsion radical polymerization. The morphology of the composite microspheres could be controlled from raspberry- and flower-like shapes, to eccentric structures by simply adjusting the feeding weight ratio of the seed to the monomer (Fe3O4/St) and varying the amount of cross-linker divinyl benzene (DVB). The morphological transition was rationalized by considering the viscosity of monomer-swollen polymer matrix and interfacial tension between the seeds and polymer matrix. Functional groups, such as carboxyl, hydroxyl, and epoxy, can be facilely introduced onto the composite microspheres through copolymerization of St with other functional monomers. The resultant microspheres displayed a high saturation magnetization (46 emu/g), well-defined core shell nanostructures, and surface chemical functionalities, as well as a sustained colloidal stability, promising for further biomedical applications.