In order to study the seismic response of underground structures when liquefied soil layer is located in different positions, the PL-Fin constitutive model proposed and developed in FLAC3D was used in this paper. The time when large deformation occurred, liquefied area distribution, the law and difference of pore water pressure and excess pore water pressure ratio, the law of the displacement characteristics, and differential settlement of structure were summarized. Their differences were also compared and analyzed when the structure is on non-liquefied soil layer. The primary conclusions are as follows: the displacement of structure was the largest when liquefied soil layer was under structure and caused the structure sink; the liquefied soil on both sides of the structure caused the structure float upward, and increased the displacement between the layers of side walls in the horizontal direction as well as between the roofs and floors in the vertical direction; the soil displacement and the displacement and differential settlement of structure were all not the largest when structure was all located over the liquefied soil, so it was not enough to only study the law when structure was embedded in liquefied soil; the law of the y-displacement of story drift on top plate was similar when the liquefied soil was located at six different positions including around the structure, on its two sides, in its bottom, in 45 degrees at the bottom of the location, on its two sides and 45 degrees at the bottom of the location, and in its bottom and 45 degrees at the bottom of the location, but the response of liquefied soil and the influence on the structure performance were different; and the large deformation caused by liquefaction occurred in 1 to 3 seconds after the jump of pore water pressure and the excess pore water pressure ratio, so their mutation can be considered as judgement on whether the large deformation occurred or not.