High transition temperature superconducting YBa2Cu3O7−x (YBCO) thin films have been epitaxially grown on YZ-cut LiNbO3 (LNO) substrates by the pulsed laser deposition technique. The interface between YBCO and LNO has been systematically investigated by scanning electron microscopy, atomic force microscopy, Auger electron spectroscopy, and x-ray photoelectron spectroscopy. Off-stoichiometry LiNbOx phases are found to segregate on the substrate surface because of lithium and oxygen vacancies formed during the high temperature YBCO growth. These submicrometer particles are observed along the Z-axis on the X-Z plane of LNO with height of ∼30 nm above the LNO surface. This rough growth surface results in YBa2Cu3O7−x thin films grown on the LNO surface that have reduced Jc and Tc, possibly limiting the use of YBCO/LNO heterostructures for surface acoustic wave (SAW) devices.