We demonstrated a facile method to control magnetite clusters with different size and surface morphology by adding bifunctional diamines. First, citrate-capped magnetites (CFe3O4) were prepared by adding citrate ions into ferrofluid during the co-precipitation process. The resulting CFe3O4 was subsequently treated by diamine molecules with different chain lengths (C-4, C-8, C-12), consequently leading to the formation of diamine-linked magnetite aggregates (DnFe3O4) with different size and surface morphology. The longer chain length of diamines increased the particle size of DnFe3O4 due to the enhanced crosslinking between CFe3O4. The excessive addition of C-4 and C-12 diamines induced the significant morphological changes from irregular-shaped CFe3O4 to spherical and rod-shaped DnFe3O4, respectively. Furthermore, DnFe3O4 retained their initial magnetism under a strong oxidative process, implicating the potential application to recyclable catalyst or active electrode materials in Li-ion batteries.