The microstructure at the interface between YBa2Cu3O7(YBCO) thin film and (100)LaAlO3 substrate has been investigated by using transmission electron microscopy. It has been observed that two distinct microstructural features existed in the interface: (1) A thin transitional layer of Ba3Al2O6 was frequently observed and the YBCO thin film grown on it showed stacking faults. (2) Sharp interface with no transitional layer was also occasionally observed and the YBCO film grown on it was single crystalline. In rare cases, a low symmetry phase was observed near the surface of the LaAlO3 substrate, however, the distortion caused by the lattice mismatch between this phase and the YBCO did not affect the quality of the YBCO thin film.