High ionic conductivity of lithium in LixLa(2-x)/3TiO3 with A-site deficient type perovskite structure has attracted considerable attention owing to both the range of practical usage (e.g., all-ceramics Li secondary batteries) and the fundamental fascination of fast lithium ion transport in crystalline solids. In present paper, we investigated the arrangement of La and vacancies in La2/3TiO3 by means of first-principles computations combined with cluster expansion approach, since it has caused a difficulty of atomistic level discussion due to numerous freedoms of configuration. The computational results predicted the alternate La concentrated and diluted layers stacking along c-axis, which agreed with the previous structural analyses. In addition, La cluster formation within ab plane is indicated. Using predicted La/vacancy arrangement, we demonstrated to calculate the Li migration path and energy profiles during Li jump by nudged elastic band method, which showed diagonal pathways to avoid passing A-site center.