The microstructure of NdNiO3 thin films deposited on Si (100) has been investigated by high resolution electron microscopy. Deposition at 250 °C and 600 °C and several annealing at high temperature under oxygen pressure were performed. Depending on the deposition temperature and annealing conditions, different texture and microstructure were observed. Relationships between microstructure and transport properties are discussed. The differences of grain boundaries are suggested to be responsible for the difference in transport properties of the films.