NdNbO4 ceramics with substituted Nd3+ were prepared by conventional mixed oxide route. The solid solubility limits of Sr, Ca, Mn, and Co in NdNbO4 were discussed. The generated second phases had a direct affect on the quality factors of NdNbO4 ceramic. The effects of ionic substitution on the microstructures and microwave dielectric properties based on structural characteristics of NdNbO4 ceramics were investigated systematically. The specimens presented single NdNbO4 phase that were used to explain the microwave dielectric properties of NdNbO4 based on the structural characteristics. From microscopy and phase analysis, it was determined the microwave dielectric properties were strongly dependent on structural characteristics. The dielectric constants were related to the relative density and ion polarizabilities, the temperature coefficients of the resonant frequency (integral) were effected by the octahedral structures, and the quality factors Qx integral was dependent on, and increased monotonically with, packing fraction.