The invention relates to the technical field of tunnel engineering and discloses a tunnel bottom prefabricated assembly type tunnel structure. The tunnel bottom prefabricated assembly type tunnel structure comprises a primary support, a secondary lining, a drainage system and a filling layer. Six protrusions are arranged on the secondary lining, and the six protrusions are arranged at intervals in the transverse direction of a tunnel. Each protrusion extends in the extending direction of the tunnel. A box type plate prefabricated block and two T type plate prefabricated blocks located on the two sides of the box type plate prefabricated plate and connected with the box type plate prefabricated block are adopted for the filling layer. The box type plate prefabricated block comprises a top plate, a left vertical plate and a right vertical plate, wherein the left vertical plate and the right vertical plate are arranged on the two sides of the lower portion of the top plate. The left vertical plate, the right vertical plate, vertical plates of the two T type plate prefabricated blocks and the ends, away from the box type plate prefabricated block, of the two T type plate prefabricated blocks are correspondingly and fixedly connected with the six protrusions. By the adoption of the tunnel structure, the diseases of the delamination, cracking, bottom bulging, sinking, mud pumping and the like of the tunnel foundation can be solved effectively, the construction pollution is reduced, and the labor production efficiency is improved. The invention further discloses a construction method of the tunnel structure.