The invention discloses a reserved shock-absorbing joint structure system and a construction method thereof. The reserved shock-absorbing joint structure system and the construction method thereof areused for improving the overall anti-seismic performance of a frame underground structure. The reserved shock-absorbing joint structure system comprises shear keys, prefabricated roofs, side walls, brackets and reserved shock-absorbing joints; the prefabricated roofs are directly placed on the brackets, contact faces are subjected to smoothing treatment, and the shear keys prevent the prefabricated roofs from falling during horizontal moving; and the reserved shock-absorbing joints among the shear keys, the brackets and the prefabricated roofs can be filled with easy-to-deform materials, whenan underground structure works normally, the two side walls bear the soil pressure at the corresponding position correspondingly, in the seismic action process, only when the reserved shock-absorbingjoints are closed, the prefabricated roofs exert the ability of transmitting the horizontal load to transmit the soil pressure acting on the certain side wall to the other side. Before the reserved shock-absorbing joints are closed, horizontal relative displacement is almost not generated between the structural roofs and bottom plates, horizontal deformation acting on columns in the structure is also reduced, and the overall anti-seismic performance of the structure is improved.