We report a facile method to synthesize magnetite nanoparticles with mesoporous structure by coprecipitation method using different stabilizing agents like salicylic acid, glutamic acid, and trichloroacetic acid. The stabilizing agents were used to prevent the aggregation of the magnetite nanocrystals and to obtain stable nanostructures even in the biological environment. The structure and morphology of magnetic nanocrystals were determined using X-ray diffraction (XRD), Fourier Transform Infrared (FTIR) spectroscopy, Brunauer-Emmett-Teller (BET) analysis, infrared (IR) spectra, scanning and transmission electron microscopy (SEM and TEM), high-resolution transmission electron microscopy (HRTEM), and selected area electron diffraction (SAED). The results reveal important differences between these magnetic nanoparticles (MNPs), which are mainly attributed to the stabilizing agents. The smallest nanoparticles were obtained in the presence of trichloroacetate ions. The mechanism of formation of these suprastructures is strongly correlated with the end functional groups of the stabilizing agent. Thus, the obtained nanoparticles are potential candidates for contrast agents as well as targeted carrier for specific diseases, especially cancer.