MgO is industrially produced from seawater or dolomite as the raw material. MgO synthesized from seawater has a relatively low impurity concentration. However, these impurities strongly affect the fine structure and physical properties (especially the thermal conductivity) of MgO. In this research, the influence of impurity concentration on the MgO grain growth and its thermal conductivity was investigated. The processing conditions for MgO powder synthesis were optimized by a polymer complex method using magnesium nitrate hydrate, citric acid, ethylene diamine, and chemical compounds containing B, Ca, or Si, which are the main impurities of MgO produced from seawater. The morphology and phase composition of the MgO powders were investigated by X-ray diffraction (XRD), field emission scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM), and energy dispersive X-ray spectroscopy (EDS). The morphological changes and differences in the thermal conductivity of MgO crystalline systems containing impurities (B, Ca, and/ or Si) were clarified, and the relationship between the fine structure of MgO crystals containing impurities and their thermal conductivities was described in detail.