Defects of barium titanate thin films synthesized on Ti-deposited substrate by the hydrothermal method were defined by the heterogeneities of the surface morphology and phase-composition. In present work, the defects observed on the films have been classified, and the feature of these defects on the morphology and phase-composition summarized, and the formation process discussed. It has been proven experimentally that the homogeneity of the films was strongly affected by the surface state of the deposited Ti layer on the Si substrate and the reaction conditions. It is important to use a defectless and well-pretreated substrate and to process at high temperature above 180°C in the Ba(OH)2solution of high concentration for long enough reaction time and is an effective way to eliminate the defects.