To control the morphology and crystal phase of iron oxide nanoparticles within several 10 nm in diameter, a microbial-derived surfactant (MDS) with a high carboxyl-group density and relatively low molecular weight (about 650 g/mol) or an artificially synthesized polyacrylic acid sodium salt (PAA) was added into the raw material aqueous solution before iron oxide particle synthesis by the gel-sol method. While pseudo-cubic hematite particles with a diameter of 500 nm were prepared without surfactant addition, spherical iron hydroxide nanoparticles with a diameter of 20 nm were prepared by MDS addition. In contrast, needle-type iron hydroxide nanoparticles with a length of 100 nm along the long axis were prepared by PAA addition. Complex formation due to the interaction between COO- groups in each surfactant and Fe3+ ions, as well as the template role prior to the synthesis of iron oxide in raw aqueous solution, inhibited the phase transition from iron hydroxide to hematite. Furthermore, the morphology of the iron hydroxide nanoparticles depended on the molecular structure of the surfactants.