The physical/chemical states and properties of nanodiamonds subjected to thermal annealing and air oxidation, which are indispensable processes for the preparation of fluorescent nanodiamonds, were investigated. Specifically, the weight loss, particle size, crystal quality, chemical bonding states of carbon and oxygen, zeta potential, dispersibility, and fluorescent and optically detected magnetic resonance (ODMR) properties were determined using X-ray diffraction (XRD) analysis, transmission electron microscopy (TEM), elemental analysis, dynamic light scattering, Raman analysis, X-ray photoelectron spectroscopy (XPS), IR spectroscopy, and a home-made fluorescence and ODMR microscope. The study focused on small-sized nanodiamonds (∼50 nm), which are applicable for biological research. The obtained results should be useful for controlling the mutually-related physical/chemical states and properties of diamond nanoparticles.