Magnetite (Fe3O4) nanoparticles has been successfully synthesized using the co-precipitation method with various pHs. The magnetites were derived from natural ironstone Kalimantan, Indonesia. The synthesis was carried out with 4 variations of precipitation pHs, i.e., 8.00; 9.06; 10.00; and 11.00. X-ray Diffraction (XRD), Scanning Electron Microscopy (SEM), High-Resolution Transmission Electron Microscopy (HRTEM), and Particle Size Analyzer (PSA) were utilized to examined the crystal structure, micro and nanostructures, and particles size distribution, respectively. The XRD results revealed that the magnetite is the dominant phase of all samples and the single phase of magnetite can be achieved with the precipitation pH > 9.06. Moreover, the particle sizes of the magnetite nanoparticles are 11, 10 and 7 nm for 9.06, 10.00, and 11.00 precipitation pH, respectively. The SEM and HRTEM images show that the particle size of ironstone and magnetite precipitates is in micro and nanoscales. The PSA results show that the particle size distribution of the magnetite nanoparticles tend to decrease with the increasing level of pH. Meanwhile, the average particle size tend to decrease with the increasing of precipitation pH,+ from 153 nm (8.00), 315 nm (9.06), 190 nm (10.00), and 153 nm (11.00). HRTEM images show that particles of Fe3O4 is spherical in shape and tend to agglomerate.