Na0.5Bi2.5Nb2O9 (NBN) based high temperature piezoelectric ceramics with A-site vacancies have been synthesized by the conventional solid state reaction method. Rietveld refinements and in-situ X-ray diffraction were performed to explore the influence of A-site vacancies on the crystalline structure and the phase evolution of NBN based ceramics with temperature, respectively. Pseudo-tetragonal distortion induced by A-site vacancies or temperature was found for the first time in the Aurivillius family, and this structural distortion might be responsible for the improvement of piezoelectric activity and the stability of piezoelectric property against thermal depolarization temperature (Td). The composition with 12 mol. % A-site vacancies exhibited good integrated performance, piezoelectric coefficient d33 and Tc were about 24.8 pC/N and 770 °C, respectively, together with excellent resistance to the thermal depolarization behavior (d33 decreased by 3% even if Td reached up to Curie temperature TC). This high temperature piezoelectric ceramics show potential applications in high temperature environments.