We previously reported that Zr substitution improves the chemical stability of Ba3Y4O9 and nominally 20 mol% Zr-substituted Ba3Y4O9 is an oxide-ion conductor at intermediate temperatures (500-700 °C). However, the influence of Zr substitution on the structural properties of Ba3Y4O9 was poorly understood. This paper aims to comprehensively understand the crystal structure of Ba3Y4O9 with Zr substitution by powder X-ray diffraction (XRD), extended X-ray absorption fine structure (EXAFS) measurements, and first-principles calculations. From the results, firstly we found that the hexagonal unit cell of Ba3Y4O9 reported in the database should be revised as doubled along the c-axis in terms of the periodicity of oxide-ion positions. The revised unit cell of Ba3Y4O9 consists of 18 layers of BaO3 and 24 layers of Y which periodically stack along the c-axis. In this work, we focused on the cationic lattice and noticed that the periodical stacking of Ba and Y layers comprises a similar sequence to that in the body-centered cubic (BCC) structure. There are two regions in the Ba3Y4O9 structure: one is a hetero-stacking region of Ba and Y layers (Ba-Y-Ba-Y-Ba) and the other is a homo-stacking region (Ba-Y-Y-Ba). It is noteworthy that the former region is similar to a cubic perovskite. In Zr-substituted Ba3Y4O9, Zr ions preferentially substitute for Y ions in the hetero-stacking region, and therefore the local environment of Zr ions in Ba3Y4O9 is quite similar to that in BaZrO3. Besides, the Zr substitution for Y in Ba3Y4O9 increases the fraction of the cubic-perovskite-like region in the stacking sequences. The structural change in the long-range order strongly affects the other material properties such as chemical stability and the ionic-conduction mechanism. Our adopted description of perovskite-related compounds based on the stacking sequence of the BCC structure should help in understanding the complex structure and developing new perovskite-related materials.