The relationship between the Li arrangement and the electrochemical behavior has been examined as a function of composition x in electrochemically lithiated A-site deficient perovskite, LixLa1/3NbO3. The cell potential diagram and powder X-ray diffraction (XRD) study indicated that the Li ions are inserted into the vacant Perovskite A-site with an electrochemical reaction. In addition, the derivatives of the cell potential diagram showed three cathodic peaks, indicating a stepwise Li insertion mechanism takes place. Such a stepwise behavior would be ascribed to the changes in arrangement of inserted Li ions in the Perovskite lattice, since the XRD patterns of pristine La1/3NbO3 showed that the La arrangement in La1/3NbO3 was ordered along the c-axis, causing two kinds of A-site vacancies. To reveal the changes in the arrangement of Li ions, the entropy measurement of the reaction was performed by both the electrochemical and the calorimetric techniques. Moreover, the formation energy of the Perovskite structure with various Li arrangements was compared by using an ab initio calculation. The results of experiment and computation suggested that the electrochemical reaction proceeded via two kinds of superstructures of Li1/6La1/3NbO3 and Li1/2La1/3NbO3 due to the ordered arrangement of Li ions.